<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/2334?offset=530 https://bioinformaticsonline.com/videolist/watch/20454/comparative-genomics-in-ensembl Wed, 21 Jan 2015 08:31:11 -0600 https://bioinformaticsonline.com/videolist/watch/20454/comparative-genomics-in-ensembl <![CDATA[Comparative Genomics in Ensembl]]> The Ensembl browser provides viewable whole-genome alignments, homologues and phylogenetic gene trees, protein families, and ancestral sequences. Learn how to view and export these data in this video.]]> https://bioinformaticsonline.com/bookmarks/view/20471/bioinformatics-scripts Thu, 22 Jan 2015 22:29:39 -0600 https://bioinformaticsonline.com/bookmarks/view/20471/bioinformatics-scripts <![CDATA[Bioinformatics Scripts]]> Some of the useful bioinformatics scripts.

For example ... contig-stats.pl is a Perl script that will automatically describe features of a sequence assembly.

http://milkweedgenome.org/?q=scripts

Address of the bookmark: http://milkweedgenome.org/?q=scripts

]]> Jit https://bioinformaticsonline.com/bookmarks/view/20504/chromevol Sun, 25 Jan 2015 00:33:11 -0600 https://bioinformaticsonline.com/bookmarks/view/20504/chromevol <![CDATA[ChromEvol]]> Chromosome number is a remarkably dynamic feature of eukaryotic evolution. Chromosome numbers can change by a duplication of the whole genome (a process termed polyploidy), or by single chromosome changes (ascending dysploidy via, e.g., chromosome fission or descending dysploidy via, e.g., chromosome fusion).
Of the various mechanisms of chromosome number change, polyploidy has received significant attention because of the impact such an event may have on the organism.
ChromEvol implements a series of likelihood models for the evolution of chromosome numbers. By comparing the fit of the different models to biological data, it may be possible to gain insight regarding the pathways by which the evolution of chromosome number proceeds. For each model, the program estimates the rates for the possible transitions assumed by the model, infers the set of ancestral chromosome numbers, and estimates the location along the tree for which polyploidy events (and other chromosome number changes) occurred. For further methodological details, see the publications and manual on the Downloads page.

http://www.tau.ac.il/~itaymay/cp/chromEvol/about.html

Address of the bookmark: http://www.tau.ac.il/~itaymay/cp/chromEvol/downloads.html

]]> Jit https://bioinformaticsonline.com/blog/view/21257/bioinformatics-phds-cover-letter Mon, 16 Feb 2015 12:48:52 -0600 https://bioinformaticsonline.com/blog/view/21257/bioinformatics-phds-cover-letter <![CDATA[Bioinformatics PhDs - Cover Letter]]> Overview
The reception your cover letter will receive is more varied and unpredictable than the other elements of your application packet.  Some readers, especially at large research universities, will skip it entirely, and focus instead on more direct indicators of your academic achievements and potential: the CV, letters, and writing sample.  Most often, however, your cover letter works in tandem with your CV, and represents your best opportunity to communicate directly with your target audience prior to an interview.

The cover letter should not simply repeat the information contained in the CV; rather it should elaborate and frame the aspects of your academic training and background that you want search committee members to have uppermost in their minds as they consider your candidacy.  At a minimum, it should contain a clear statement of your research and teaching interests, and how your qualifications match the requirements of the job description. Many disciplines have their own conventions and protocols for application materials including the cover letter. Be sure to show a draft of your letter to your chair or the department's placement advisor.

There is no perfect or even preferred style of cover letter save that tone should be that of a confident professional.  Departments aren't interested in hiring graduate students (they already have enough of those).  They are looking for serious scholars/teachers who will make interesting, congenial, and productive colleagues. While it is probably not a good use of your time to tailor your letter for each opening, you will probably need at least two base versions that emphasize different elements (You would not want to use the same cover letter to apply to Oberlin as UC Irvine). You may want to customize the letters for the three to five jobs most attractive to you.

Your cover letter should not exceed a page and a half or two at the most.  No one will read a four-page letter, and your apparent inability to communicate your credentials in a concise manner is not to your advantage. Every line of your letter should serve a demonstrable purpose. Some people have gotten excellent jobs with a brief, boilerplate letter containing no more than a short intro, a paragraph on their research, and a couple of sentences on their teaching. Others use letters that discuss in very specific terms how they, their research, and their teaching would "fit" within the existing department and institutional setting. The choice of style is up to you, and should reflect what makes you feel most comfortable and most positive about your credentials.

There are, however, circumstances where a longer, more annotated version is more likely to be helpful. The issues you should take into account when making this decision are:

    The size of the department/institution
    The extent to which your research is mainstream and its significance readily apparent
    The extent to which your qualifications diverge from those mentioned in the job ad
    The extent to which the institution to which you are applying differs from UC Berkeley and the relative importance of teaching versus research
    Unusual circumstances or career paths

Size matters. The larger the department, the less detailed your letter needs to be.  If there are already six people working in your sub-field, they can assess and translate the significance of your work to others in the department.  If, however, you will be the only history of science person or the only physical anthropologist in the department, the search committee and others will likely need more help from you to understand the import of your work.  Remember, if they are searching for your specialty they are understaffed in your area, and even if there is more than one person in your sub-field she/he may be on leave or otherwise uninvolved in the search.

Similarly, smaller departments are more likely to be concerned than larger ones about the specific courses you are prepared to teach.  If there are certain core courses your position needs to cover, make it unambiguously clear that you are prepared to do so even if you haven't taught them already.

As a rule of thumb, the more your profile diverges from the specifics of the job description (or the norm, such that it exists), the more likely you will want to say more about why you are nonetheless a strong candidate.  By doing so you can turn a question mark into an advantage.  Highlight your strengths, and if you have time perform a little research on the department (see below) so you can explain how you would add to the department in ways that they might otherwise not have considered.  Job descriptions are not always etched in stone. If you're very interested in the job, call the department and ask to speak to someone on the search committee.  If that's too intimidating, call the departmental assistant or secretary. They can at least tell you if it’s a new position or replacement which in turn can indicate whether they really need someone who can teach The Politics of Southern Africa or if Middle Eastern Politics would do just as well.  They may well be willing to sacrifice a course in an area that the ad specified in order to get the extra teaching experience or innovative research that you have to offer, but only if you give them the opportunity and explain what they'd get in return.

 If you've taken an unusually long time to finish because you spent three years learning a new language in order to prepare for two years of original research or some other factor that enriches what you have to offer as a teacher or a scholar, let them know about it.  Learning a new language, for example, is an indicator of your commitment to serious scholarship.  Think of a way to put a positive valence on an aspect of your CV that you believe is likely to raise questions or doubts.

As hard as it may be for not-yet-employed-but-soon-to-be academics like yourselves to believe, there are some individuals and departments that are intimidated by you and your institutional pedigree.  There are many fine schools and departments that are convinced that every Berkeley graduate student is only interested in a position at Harvard, Princeton, or (hold your nose) Stanford.  If it is a small liberal arts college, they may also assume that you view teaching and advising undergraduates strictly as a necessary evil. Ergo, why interview someone who will either look down their nose at us, and/or desert us for greener pastures as soon as their third book has been published and Yale comes calling.  They often don't seem to realize that Berkeley graduate students are sincerely interested in a wide range of academic settings for a variety of reasons personal and professional, and, perhaps more to the point, Yale rarely "comes calling."  An even greater burden of proof exists if a quick scan of your CV reveals that your all of your experience in higher education has occurred in a large, elite, research-oriented setting. How can you overcome this potential obstacle especially if you're very interested in a school that you have reason to believe may be suspicious of Berkeley PhDs?

It's probably not advisable to write in a cover letter that they shouldn't be intimidated by lil' old you (i.e., "I'm really not very good; in fact, my advisor says I'm her worst graduate student in twenty years."), but there are ways to indicate a sincere interest in their department.  One means is to do a little research, and briefly discuss how you might fit into the department and the institutional community-at-large.  There are numerous articles written by faculty about the search process that state explicitly the positive impact it can have on their impression of a candidate to see evidence that that he/she has taken the time to learn something about them. Researching a department and its associated programs/research centers has never been easier.  Virtually all colleges and universities are online, and their web addresses can be easily located using Education/Universities link.

A second way to address fears of imminent flight is to provide evidence of ties to the area, the university, or lifestyle.   If you are from the Midwest, have family nearby, or even if you just spent an enjoyable summer there, add a line about it and your desire to return to your cover letter for Purdue or Wayne State.  If you did your undergraduate work at a similar type of institution, draw their attention to that link.  Don't assume that they will notice where you got your BA on your CV, and make the connection.

If you are applying to small, liberal arts colleges, don't just list the courses you've taught with a line of boilerplate about how important you take your teaching responsibilities to be. These days, a good, small college has a list price of about $30,000 a year, and close contact with people like you is one of their key selling points to parents and potential students. You are expected to be more than a lecturer, and your ability to convey your recognition of that fact and a sincere interest in working closely with students matters. Advising, participating in non-academic activities, watching your students grow and mature inside the classroom and out (and having an influence on that process) can be among the most rewarding aspects of the profession.  If you value these broader elements of being a professor, let them know. In particular, if your own experience has been limited to large universities, think about describing an episode where you had a positive impact on the development of a student and the satisfaction you derived from helping him or her. At many small colleges, and large universities (including Berkeley) as well, one of the most significant pedagogical trends is fostering greater student involvement in faculty research.  If you can articulate how this might occur for you and their students in a brief but thoughtful manner, it can alleviate some of the concerns occasioned by your Berkeley background.

Your letter typically will have four segments: the introduction, research, teaching, and the closing.

Introduction
Be sure to identify the position you are applying for by rank and sub-field in the first sentence or two.  It is not uncommon for departments to be engaged in more than one search in a given year, and large departments may have more than one in your sub-field.  If it is an open rank position and you are applying as an assistant professor, in most cases you and your record of accomplishments will not be directly compared with those of more experienced candidates applying for it at the associate or full professor level.  Rather, applicants are assessed based on where they are in their career path, and you have every chance of successfully competing against them.

If you have finished, mention it up front. If not, state when you expect to file - no later than June 2003.  Many readers will view your optimistic prediction with a skeptical eye, and anything you can say that makes the claim appear more credible (e.g., "I have written and my chair has reviewed four of the six chapters.") can help mitigate their concerns.  You can put such a statement in the introduction or wait until you discuss the dissertation itself.

If your discipline holds its annual meeting in the summer or early fall (i.e., before application deadlines) and you had an excellent conference interview, make reference to it in the cover letter including the names of the faculty with whom you spoke.  By the time people actually start to read files, months may have passed and even the strongest of impressions can fade.  But they can be rehabilitated and revived, especially if you can remind them of a specific strength, ability, or issue that seemed particularly salient during the interview.
Research
Unless you are applying to a school that cares only about your teaching (increasingly rare), a description of your research generally follows next.  The challenge here is not simply to describe your research, but to frame it in terms of your sub-field and discipline. The search committee, hasn't lived, eaten and breathed Post-Edwardian Hermeneutics for the past five years the way you have. And they haven't been there every step of the torturous process like your friends and significant others. So forgive them for not immediately recognizing your research at first blush for the path-breaking work that it is.

Departments want to know that in hiring you, they are adding someone who will make a future contribution to the discipline and enhance the reputation of the department. However, they are often ill-equipped to understand exactly how that will be true in your particular case. Many disciplines are sufficiently broad that leading or cutting-edge research in one sub-field is barely intelligible to those in others.  In addition, when you became a candidate for the short list, your file will be read by department members outside your specialty, and, oftentimes later on in the process, by individuals outside your discipline as well. You need to describe the forest in which your tree resides, and explain why it matters in terms of the broader trends and issues within your discipline. Obviously, if your work is focused on one of the classic conundrums of your field, much less in the way of providing perspective is necessary than if you are addressing an emergent issue or employing an unconventional approach.

If your research is particularly novel or cutting-edge, any markers of broader acceptance by other, more established scholars or scholarly organs in your field can ameliorate possible concerns about its relevance and potential importance.  In discussing your work, note the recognition it has received in the form of competitive grants, awards, publications in refereed journals, and/or presentations at major conferences.

It is also important to mention where you expect your research to go after the completion of your dissertation and the publications that will flow from it.  They, especially at research-oriented institutions, want to know at least in broad terms where you expect to go from here.  They want to see evidence of a scholarly agenda that extends beyond the dissertation.  You don't need to have pages written or titles blocked out, but you need to tell them in a paragraph, (two at the most) about what questions intrigue you, and how you expect to go about finding the answers to them.  These questions for future research may have been generated by the findings of your dissertation, unusual data uncovered during your fieldwork, or interesting side issues that you were forced to put off in order to keep your dissertation taut and focused.  Think twice about mentioning future projects that appear entirely unrelated to your current work. Departments will want you to be firmly established in one area before you go off into another.

The relative importance of teaching versus research is a continuous and not a discrete variable.  Even schools that emphasize teaching in their job listing will generally want evidence of scholarly engagement and publishing potential. It is a very competitive market for students out there, and virtually all institutions are under pressure to sell themselves via the quality of their faculty to the limited number of good students in the applicant pool.  A good marker for the relative importance of teaching versus research is the teaching load.  An institution with a 3-2 teaching load (a total of five courses taught per two-semester year) will expect more in the way of and value research more highly than one with a 3-3 load.

If you work in a capital-intensive area, mention your track record of gaining grants and other sources of external funding.
Teaching
In a similar fashion, the more the institution you are applying to diverges from Berkeley and the more your profile differs from the job description, the more expansive you should be in talking about your teaching and what you have to offer their students.  If you have won a teaching award at Berkeley, don't make them wait until they read your CV to discover that fact.

For letters sent to large universities where you will be expected to teach large, lecture courses and graduate seminars, little is needed except to convey that you have the necessary experience and/or background.  Since the dominant pedagogical style is the same as that found at Berkeley, it will be assumed that you will be able to do the same for them.

If you have TA'd some of the courses that (based on the job description) you would be expected to offer, let them know.  If you have not had that opportunity, but your fields and research fall within the domain of the job description, you may want to add a line about how well prepared you are to teach such courses based on your training and research.

If your profile does not correspond exactly to the description found in the job announcement, but you believe that you could nonetheless teach the required courses, explain the basis for your confidence. What strength would you bring to the department that would more than make up for your "otherness"?  Departments may decide that they don't "need" another conventional European historian if you can convince them that you can handle the core courses and offer something new that they don't currently cover as well. In this case especially, think about doing some research so you can speak in more specific terms about how you would fit into and enhance the department's offerings. Help them visualize how you would strengthen them as a department.

Small colleges will want to know that you are able to teach on a more intimate basis and are prepared to take the time to do it well. If you give them three generic lines about how "important" you consider your teaching responsibilities, don't expect much of a positive response.  Spend a couple of paragraphs describing your teaching experience and philosophy, and how you would take advantage of the opportunity to create you own courses.

If you've had the opportunity to design and teach your own course, tell them, briefly, how you went about it and the choices you made. Don't just say you're a good teacher, tell them why. Look over your teaching evaluations and pick out one or two consistent strengths to highlight. Drawing on your experience, talk about how you engage students and enhance their skills (especially writing) and intellectual development.

For good, small colleges, the quality of the teaching offered to students is their stock-in- trade.  Even the most research-oriented, small colleges take teaching undergraduates very seriously. You need to demonstrate that you take it seriously as well, and can talk about it using more than vague generalities and shop-worn cliches.
Closing/Enclosures
Wrap it up quickly.  If you are going to be traveling for any significant portion of the job search season be sure to let them know how they can contact you (email, cellphone and/or a Pacific Bell message center account are particularly good options).

Before closing, include a sentence where you list the materials you have enclosed (e.g., CV, dissertation abstract, transcripts, teaching statement/portfolio, writing samples, etc.) and are having sent separately (letters of recommendation).  You will often be assembling multiple packets at the same time (as in midnight October 14th, midnight November 14th, etc.) for jobs that ask for different combinations of enclosures.  In addition to telling them what they should have received, it serves as a handy list for you to check before sealing the envelope.

Should you send a writing sample, even if they haven't asked for one? Unless the norm in your discipline is to never send more than they ask for, if you've been smart and have already run off thirty copies at two cents per page (that's only sixty cents for a thirty page chapter) by all means send it.  That way it's in the file should someone become interested in you and want to read more.

]]> Martin Jones https://bioinformaticsonline.com/news/view/21312/r-for-microsoft-excel Wed, 18 Feb 2015 00:43:27 -0600 https://bioinformaticsonline.com/news/view/21312/r-for-microsoft-excel <![CDATA[R for Microsoft Excel]]>

If you currently use a spreadsheet like Microsoft Excel for data analysis, you might be interested in taking a look at this tutorial on how to transition from Excel to R by Tony Ojeda. The tutorial explains how to use R functions in place of Excel formulas, including tools like =AVERAGE and =VLOOKUP. For the most part, it uses modern R packages to keep the R code clear and concise.

You'll likely still be using Excel as a data source, though, so you'll also want to check out this guide to importing data from Excel to R from MilanoR.

Reference http://www.r-bloggers.com/an-r-tutorial-for-microsoft-excel-users/

]]> Jitendra Narayan https://bioinformaticsonline.com/pages/view/21367/a-guide-for-complete-r-beginners-r-syntax Fri, 20 Feb 2015 23:41:03 -0600 https://bioinformaticsonline.com/pages/view/21367/a-guide-for-complete-r-beginners-r-syntax <![CDATA[A guide for complete R beginners :- R Syntax]]> R is a functional based language, the inputs to a function, including options, are in brackets. Note that all dat and options are separated by a comma

  • Function(data, options)

Even quit is a function

  • q()

So is help

help(read.table)

Provides the help page for the FUNCTION ‘read.table’

help.search(“t test”)

Searches for help pages that might relate to the phrase ‘t test’

NOTE: quotes are needed for search strings, they are not needed when referring to data objects or function names.

There is a short cut for help,

? shows the help page on a function name, same as help(function)

?read.table

?? searches for help pages on functions, same as help.search(‘phrase’)

??“t test”

Information is usually returned from a function, by default this is printed to screen

read.table(‘data.tsv’)

This can always be stored, we call what it is stored in an ‘object’

mydata

here mydata is an object of type dataframe

Reminder:

  • Vector: a list of numbers, equivalent to a column in a table
  • Data Frame = a collection of vectors. Equivalent to a table

Hint:

  • Up/Down arrow keys can be use to cycle through previous commands
]]> Archana Malhotra https://bioinformaticsonline.com/opportunity/view/21472/asst-professor-at-central-university-of-jharkhand-cuj Sun, 01 Mar 2015 01:17:52 -0600 <![CDATA[Asst. Professor at Central University of Jharkhand (CUJ)]]> Central University of Jharkhand (CUJ) has issued a recruitment notification for the recruitment of Assistant Professor through recruitment notification – Central University of Jharkhand (CUJ) Recruitment 2015 – Advt. No.: CUJ/Advt./14-15/15 Date: 26th Feb. 2015. Candidates who have completed M.Sc, Ph.D can apply for the new recruitment notification from Central University of Jharkhand (CUJ)

Central University of Jharkhand has been granted funds by the Department of Biotechnology (DBT), Govt. of India to establish “DBT-Boost to CUJ Interdisciplinary Life Sciences Departments for Education and Research” Applications are invited for the Assistant Professor on purely temporary basis. The appointments shall be initially for a period of one year, renewable every year depending on the satisfactory performance, till the end of project.

Position: ASSISTANT PROFESSOR (Total 03)
Salary: 45,000/- (fixed) per month
Essential Qualifications: i. Good academic record with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed) at the master’s degree level with specialization in Biodiversity and Systematic/ Systems Biology/ Biophysics/ Bioinformatics from an Indian University, or an equivalent degree from an accredited foreign university. ii. Besides fulfilling the above qualifications, the candidates must have cleared the National Eligibility Test (NET) conducted by the UGC, CSIR or similar test accredited by the UGC like SLET/SET. iii. Notwithstanding anything contained in i. and ii. candidates, who are or have been awarded Ph.D Degree in accordance with the University Grants Commission (Minimum Standards and Procedure for Award of Ph.D. Degree) Regulation, 2009, shall be exempted from therequirement of the minimum eligibility condition of NET/SLET/SET for recruitment and appointment of Assistant Professor. iv. NET/SLET/SET shall also not be required for such disciplines for which NET/SLET/SET in not conducted.
Desirable: Preference will be given to candidates having Ph.D in any of the above mentioned areas with NET

IMPORTANT DATES TO REMEMBER :

Last Date to Apply for this job 24/3/2015

REFERENCE:

Central University of Jharkhand (CUJ) Recruitment 2015 – Advt. No.: CUJ/Advt./14-15/15 Date: 26th Feb. 2015.

More at http://cuj.ac.in/careers.php

]]> https://bioinformaticsonline.com/news/view/22133/r-320-is-released Sat, 18 Apr 2015 05:06:44 -0500 https://bioinformaticsonline.com/news/view/22133/r-320-is-released <![CDATA[R 3.2.0 is released]]> R 3.2.0 (codename “Full of Ingredients”) was released yesterday. You can get the latest binaries version from here. (or the .tar.gz source code from here). The full list of new features and bug fixes is provided below.

Upgrading to R 3.2.0 on Windows

If you are using Windows you can easily upgrade to the latest version of R using the installr package. Simply run the following code:

# installing/loading the latest installr package:
install.packages("installr"); library(installr) #load / install+load installr
 
updateR() # updating R.

Running “updateR()” will detect if there is a new R version available, and if so it will download+install it (etc.).

If you are an R blogger yourself you are invited to add your own R content feed to this site (Non-English R bloggers should add themselves- here)

NEW FEATURES

  • anyNA() gains a recursive argument.
  • When x is missing and names is not false (including the default value), Sys.getenv(x, names) returns an object of class "Dlist" and hence prints tidily.
  • (Windows.) shell() no longer consults the environment variable SHELL: too many systems have been encountered where it was set incorrectly (usually to a path where software was compiled, not where it was installed). R_SHELL, the preferred way to select a non-default shell, can be used instead.
  • Some unusual arguments to embedFonts() can now be specified as character vectors, and the defaults have been changed accordingly.
  • Functions in the Summary group duplicate less. (PR#15798)
  • (Unix-alikes.) system(cmd, input = ) now uses ‘shell-execution-environment’ redirection, which will be more natural if cmd is not a single command (but requires a POSIX-compliant shell). (Wish of PR#15508)
  • read.fwf() and read.DIF() gain a fileEncoding argument, for convenience.
  • Graphics devices can add attributes to their description in .Device and .Devices. Several of those included with R use a "filepath" attribute.
  • pmatch() uses hashing in more cases and so is faster at the expense of using more memory. (PR#15697)
  • pairs() gains new arguments to select sets of variables to be plotted against each other.
  • file.info(, extra_cols = FALSE) allows a minimal set of columns to be computed on Unix-alikes: on some systems without properly-configured caching this can be significantly faster with large file lists.
  • New function dir.exists() in package base to test efficiently whether one or more paths exist and are directories.
  • dput() and friends gain new controls hexNumeric and digits17 which output double and complex quantities as, respectively, binary fractions (exactly, see sprintf("%a")) and as decimals with up to 17 significant digits.
  • save(), saveRDS() and serialize() now support ascii = NA which writes ASCII files using sprintf("%a") for double/complex quantities. This is read-compatible with ascii = TRUE but avoids binary->decimal->binary conversions with potential loss of precision. Unfortunately the Windows C runtime’s lack of C99 compliance means that the format cannot be read correctly there in R before 3.1.2.
  • The default for formatC(decimal.mark =) has been changed to be getOption("OutDec"); this makes it more consistent with format() and suitable for use in print methods, e.g. those for classes "density", "ecdf", "stepfun" and "summary.lm".

    getOption("OutDec") is now consulted by the print method for class "kmeans", by cut(), dendrogram(), plot.ts() and quantile() when constructing labels and for the report fromlegend(trace = TRUE).

    (In part, wish of PR#15819.)

  • printNum() and hence format() and formatC() give a warning if big.mark and decimal.mark are set to the same value (period and comma are not uncommonly used for each, and this is a check that conventions have not got mixed).
  • merge() can create a result which uses long vectors on 64-bit platforms.
  • dget() gains a new argument keep.source which defaults to FALSE for speed (dput() and dget() are most often used for data objects where this can make dget() many times faster).
  • Packages may now use a file of common macro definitions in their help files, and may import definitions from other packages.
  • A number of macros have been added in the new ‘share/Rd’ directory for use in package overview help pages, and promptPackage() now makes use of them.
  • tools::parse_Rd() gains a new permissive argument which converts unrecognized macros into text. This is used by utils:::format.bibentry to allow LaTeX markup to be ignored.
  • options(OutDec =) can now specify a multi-byte character, e.g., options(OutDec = "u00b7") in a UTF-8 locale.
  • is.recursive(x) is no longer true when x is an external pointer, a weak reference or byte code; the first enables all.equal(x, x) when x .
  • ls() (aka objects()) and as.list.environment() gain a new argument sorted.
  • The "source" attribute (which has not been added to functions by R since before R version 2.14.0) is no longer treated as special.
  • Function returnValue() has been added to give on.exit() code access to a function’s return value for debugging purposes.
  • crossprod(x, y) allows more matrix coercions when x or y are vectors, now equalling t(x) %*% y in these cases (also reported by Radford Neal). Similarly, tcrossprod(x,y) and %*% work in more cases with vector arguments.
  • Utility function dynGet() useful for detecting cycles, aka infinite recursions.
  • The byte-code compiler and interpreter include new instructions that allow many scalar subsetting and assignment and scalar arithmetic operations to be handled more efficiently. This can result in significant performance improvements in scalar numerical code.
  • apply(m, 2, identity) is now the same as the matrix m when it has named row names.
  • A new function debuggingState() has been added, allowing to temporarily turn off debugging.
  • example() gets a new optional argument run.donttest and tools::Rd2ex() a corresponding commentDonttest, with a default such that example(..) in help examples will run donttest code only if used interactively (a change in behaviour).
  • rbind.data.frame() gains an optional argument make.row.names, for potential speedup.
  • New function extSoftVersion() to report on the versions of third-party software in use in this session. Currently reports versions of zlib, bzlib, the liblzma from xz, PCRE, ICU, TRE and the iconv implementation.

    A similar function grSoftVersion() in package grDevices reports on third-party graphics software.

    Function tcltk::tclVersion() reports the Tcl/Tk version.

  • Calling callGeneric() without arguments now works with primitive generics to some extent.
  • vapply(x, FUN, FUN.VALUE) is more efficient notably for large length(FUN.VALUE); as extension of PR#16061.
  • as.table() now allows tables with one or more dimensions of length 0 (such as as.table(integer())).
  • names(x) now clears the names of call and ... objects.
  • library() will report a warning when an insufficient dependency version is masking a sufficient one later on the library search path.
  • A new plot() method for class "raster" has been added.
  • New check_packages_in_dir_changes() function in package tools for conveniently analyzing how changing sources impacts the check results of their reverse dependencies.
  • Speed-up from Peter Haverty for ls() and methods:::.requirePackage() speeding up package loading. (PR#16133)
  • New get0() function, combining exists() and get() in one call, for efficiency.
  • match.call() gains an envir argument for specifying the environment from which to retrieve the ... in the call, if any; this environment was wrong (or at least undesirable) when thedefinition argument was a function.
  • topenv() has been made .Internal() for speedup, based on Peter Haverty’s proposal in PR#16140.
  • getOption() no longer calls options() in the main case.
  • Optional use of libcurl (version 7.28.0 from Oct 2012 or later) for Internet access:
    • capabilities("libcurl") reports if this is available.
    • libcurlVersion() reports the version in use, and other details of the "libcurl" build including which URL schemes it supports.
    • curlGetHeaders() retrieves the headers for http://, https://, ftp:// and ftps:// URLs: analysis of these headers can provide insights into the ‘existence’ of a URL (it might for example be permanently redirected) and is so used in R CMD check --as-cran.
    • download.file() has a new optional method "libcurl" which will handle more URL schemes, follow redirections, and allows simultaneous downloads of multiple URLs.
    • url() has a new method "libcurl" which handles more URL schemes and follows redirections. The default method is controlled by a new option url.method, which applies also to the opening of URLs via file() (which happens implicitly in functions such as read.table.)
    • When file() or url() is invoked with a https:// or ftps:// URL which the current method cannot handle, it switches to a suitable method if one is available.
  • (Windows.) The DLLs ‘internet.dll’ and ‘internet2.dll’ have been merged. In this version it is safe to switch (repeatedly) between the internal and Windows internet functions within an Rsession.

    The Windows internet functions are still selected by flag –internet2 or setInternet2(). This can be overridden for an url() connection via its new method argument.

    download.file() has new method "wininet", selected as the default by –internet2 or setInternet2().

  • parent.env<- can no longer modify the parent of a locked namespace or namespace imports environment. Contributed by Karl Millar.
  • New function isLoadedNamespace() for readability and speed.
  • names(env) now returns all the object names of an environment env, equivalently to ls(env, all.names = TRUE, sorted = FALSE) and also to the names of the corresponding list,names(as.list(env, all.names = TRUE)). Note that although names() returns a character vector, the names have no particular ordering.
  • The memory manager now grows the heap more aggressively. This reduces the number of garbage collections, in particular while data or code are loaded, at the expense of slightly increasing the memory footprint.
  • New function trimws() for removing leading/trailing whitespace.
  • cbind() and rbind() now consider S4 inheritance during S3 dispatch and also obey deparse.level.
  • cbind() and rbind() will delegate recursively to methods::cbind2 (methods::rbind2) when at least one argument is an S4 object and S3 dispatch fails (due to ambiguity).
  • (Windows.) download.file(quiet = FALSE) now uses text rather than Windows progress bars in non-interactive use.
  • New function hsearch_db() in package utils for building and retrieving the help search database used by help.search(), along with functions for inspecting the concepts and keywords in the help search database.
  • New function .getNamespaceInfo(), a no-check version of getNamespaceInfo() mostly for internal speedups.
  • The help search system now takes keyword entries in Rd files which are not standard keywords (as given in ‘KEYWORDS’ in the R documentation directory) as concepts. For standard keyword entries the corresponding descriptions are additionally taken as concepts.
  • New lengths() function for getting the lengths of all elements in a list.
  • New function toTitleCase() in package tools, tailored to package titles.
  • The matrix methods of cbind() and rbind() allow matrices as inputs which have 2^31 or more elements. (For cbind(), wish of PR#16198.)
  • The default method of image() has an explicit check for a numeric or logical matrix (which was always required).
  • URLencode() will not by default encode further URLs which appear to be already encoded.
  • BIC(mod) and BIC(mod, mod2) now give non-NA numbers for arima() fitted models, as nobs(mod) now gives the number of “used” observations for such models. This fixes PR#16198, quite differently than proposed there.
  • The print() methods for "htest", "pairwise.htest" and "power.htest" objects now have a digits argument defaulting to (a function of) getOption("digits"), and influencing all printed numbers coherently. Unavoidably, this changes the display of such test results in some cases.
  • Code completion for namespaces now recognizes all loaded namespaces, rather than only the ones that are also attached.
  • The code completion mechanism can now be replaced by a user-specified completer function, for (temporary) situations where the usual code completion is inappropriate.
  • unzip() will now warn if it is able to detect truncation when unpacking a file of 4GB or more (related to PR#16243).
  • methods() reports S4 in addition to S3 methods; output is simplified when the class argument is used. .S3methods() and methods::.S4methods() report S3 and S4 methods separately.
  • Higher order functions such as the apply functions and Reduce() now force arguments to the functions they apply in order to eliminate undesirable interactions between lazy evaluation and variable capture in closures. This resolves PR#16093.

More at http://cran.rstudio.com/

Reference: http://www.r-bloggers.com/r-3-2-0-is-released-using-the-installr-package-to-upgrade-in-windows-os/

]]> Neel https://bioinformaticsonline.com/researchlabs/view/22410/nicolas-corradi-lab Tue, 26 May 2015 16:19:02 -0500 <![CDATA[Nicolas Corradi Lab]]> The goal of our research is to better understand the biology of microbial organisms of significant ecological, veterinary and medical importance.
To achieve this goal, our team combines the power of next generation DNA sequencing and bioinformatics with molecular biology and experimental procedures.

Main research topics:
- Comparative and Population Genomics of Plant Symbionts
- Parasite Genome Evolution
- Experimental Evolution of Microbial Symbionts and Parasites
- Phylogenomics of Early Branching Fungi

More at http://corradilab.weebly.com/

]]> https://bioinformaticsonline.com/pages/view/22567/rosalind-problem-solution-with-perl Tue, 09 Jun 2015 23:35:18 -0500 https://bioinformaticsonline.com/pages/view/22567/rosalind-problem-solution-with-perl <![CDATA[Rosalind Problem Solution with Perl]]> Rosalind is a platform for learning bioinformatics and programming through problem solving. Take a tour to get the hang of how Rosalind works.

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