The OpenCPU JavaScript client library provides the most seamless integration of R and JavaScript available today.

OpenCPU uses standard R packaging to develop, ship and deploy web applications. Several open source example apps are available from Github.

Installing your own OpenCPU server is super easy and only takes a few minutes.

More at https://www.opencpu.org/

The group is both computational and experimental.

We ask biological questions to large datasets made using novel genomics techniques, with the help of computers. One of the strengths in the group are the many connections to high-profile experimental laboratories which supply data to be analyzed.

Lab webpage @ http://people.binf.ku.dk/albin/Sandelin_group_at_the_Bioinformatic_Centre/The_Sandelin_group.html

the study of the sequence-structure relationship
(application -> structure prediction)
the study of the structure-function relationship
(application -> function prediction)

Therefore, anything related to the configuration (sequence) and conformation (structure) in atomic systems of proteins and nucleic acids, and the interaction of these with other elements (function) is of our major interest.

Lab page @ http://melolab.org/mbl/

Lab Page http://gabi.cidbio.org/index/

Translational recoding.

RNA editing.

Evolution of the genetic code and translation.

More at http://lapti.ucc.ie/research.html

Lab page http://lapti.ucc.ie/index.html

Now, two research groups have engineered new optogenetic proteins that can be used to efficiently silence neurons. One of the two new proteins comes from the lab of Karl Deisseroth, a psychiatrist and neuroscientist at Stanford University who helped develop optogenetics as a research tool. His group’s new “off” switch for neurons was created by changing 10 of the 333 amino acids in an existing optogenetic protein, which itself had been engineered by combining natural proteins from green algae. That advance “creates a powerful tool that allows neuroscientists to apply a brake in any specific circuit with millisecond precision,” said Thomas Insel, director of the National Institute of Mental Health, in a released statement. The other new silencing protein, developed by scientists at the Humboldt University of Berlin and collaborators, was created by changing amino acids in the same existing optogenetic protein. 

Some researchers are also looking to optogenetics as a potential treatment for patients with a variety of conditions (see “For Mice, and Maybe Men, Pain Is Gone in a Flash,” and “Flipping on the Lights to Halt Seizures”) but there are huge challenges to overcome. The method requires genetic modification of cells to make them light-sensitive. It also requires implanted light sources for all but the shallowest of nerve endings.

The Indian scientists working in Bangalore, along with their American counterparts, have mapped more than 17,000 proteins in 30 organs of the human body. Just like the human genome was sequenced around the turn of the millennium, this is an equivalent mapping of the human proteome.

The researcher estimated there are around 20,500 proteins in the human body. These scientists have profiled around 17,294, which account for around 84% of the total proteins. Apart from this, the team also traced around 2,500 of 3,000 proteins that had been categorised as "missing proteins".

The work, done by group of Indian scientists, and Johns Hopkins University, published in the renowned journal Nature ( http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html ). Of the 72 people who worked on the project, 46 are Indians.

Reference:

http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html

http://www.proteinatlas.org/ -The antibody-based Human Protein Atlas programme

http://www.humanproteomemap.org/ -Proteogenomic analysis by identifying translated proteins from annotated pseudogenes, non-coding RNAs and untranslated regions.

https://www.proteomicsdb.org/ -Assembled protein evidence for 18,097 genes in ProteomicsDB

This is a short post giving steps on how to actually install R packages. Let’s suppose you want to install the ggplot2 package. Well nothing could be easier. We just fire up an R shell and type:

> install.packages("ggplot2")

In theory the package should just install, however:

• if you are using Linux and don’t have root access, this command won’t work.
• you will be asked to select your local mirror, i.e. which server should you use to download the package.

Installing packages without root access

First, you need to designate a directory where you will store the downloaded packages. On my machine, I use the directory /data/Rpackages/ After creating a package directory, to install a package we use the command:

> install.packages("ggplot2", lib="/data/Rpackages/")
> library(ggplot2, lib.loc="/data/Rpackages/")


It’s a bit of a pain having to type /data/Rpackages/ all the time. To avoid this burden,  we create a file .Renviron in our home area, and add the line R_LIBS=/data/Rpackages/ to it. This means that whenever you start R, the directory /data/Rpackages/ is added to the list of places to look for R packages and so:

> install.packages("ggplot2")
> library(ggplot2)

just works!

Setting the repository

Every time you install a R package, you are asked which repository R should use. To set the repository and avoid having to specify this at every package install, simply:

• create a file .Rprofile in your home area.
• Add the following piece of code to it:


cat(".Rprofile: Setting UK repositoryn")
r = getOption("repos") # hard code the UK repo for CRAN
r["CRAN"] = "http://cran.uk.r-project.org"
options(repos = r)
rm(r)


I found this tip in a stackoverflow answer .

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/