BOL: Related items

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

Jit — Tue, 07 Nov 2017 04:36:10 -0600

We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia stipitis. More than 95% of the genome is recovered, with no errors; half the assembled sequence is in contigs longer than 101 kilobases and in scaffolds longer than 269 kilobases. Incorporating fosmid ends recovers entire chromosomes. Meraculous relies on an efficient and conservative traversal of the subgraph of the k-mer (deBruijn) graph of oligonucleotides with unique high quality extensions in the dataset, avoiding an explicit error correction step as used in other short-read assemblers. A novel memory-efficient hashing scheme is introduced. The resulting contigs are ordered and oriented using paired reads separated by ∼280 bp or ∼3.2 kbp, and many gaps between contigs can be closed using paired-end placements. Practical issues with the dataset are described, and prospects for assembling larger genomes are discussed.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158087/

SENIOR RESEARCH FELLOW at All India Institute of Medical Sciences (AIIMS Delhi) - Delhi, Delhi

Wed, 11 Mar 2015 03:06:10 -0500

Applications are invited from eligible candidates for the following temporary post in an ICMR funded Research Project entitle “An Investigation to find out reasons for Phenotypic Heterogeneity/Variability in 22q11.2 Microdeletion Syndrome” in Department of Reproductive Biology, AIIMS, New Delhi PI: Dr. Ashutosh Halder, Professor, Department of Reproductive Biology

Name of the post: Senior Research Fellow (SRF)
Duration: 2 year
Salary: Rs. 28000/- per month + 30% HRA
Eligibility: MSc (life sciences) with 2 years research experience, NET/GATE qualified
Desirable: Experience in the field of Genomics, Epigenomics & Bioinformatics
SELECTION PROCEDURE FOR ALL INDIA INSTITUTE OF MEDICAL SCIENCES (AIIMS DELHI) – SENIOR RESEARCH FELLOW POST:

Candidates can apply on or before 15/03/2015
No Detailed information about the selection process is mentioned in the recruitment notification
HOW TO APPLY FOR SENIOR RESEARCH FELLOW VACANCY IN ALL INDIA INSTITUTE OF MEDICAL SCIENCES (AIIMS DELHI):

Deadline: 15.03.15 Submit your C.V in Room No. 2099 (Molecular Cytogenetics Lab), 2nd floor, Reproductive Biology, All India Institute of Medical Sciences, New Delhi-110029 or Email CV to: ashutoshhalder@gmail.com Your CV should include the details of your work experience & degrees along with two references with e-mail and contact number Only 10 shortlisted (on merit) candidates will be invited for interview. No TA/DA will be applicable for the same

HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning

Abhimanyu Singh — Tue, 01 Jan 2019 12:01:00 -0600

HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read alignments.

HECIL’s core algorithm by introducing an iterative learning paradigm that enhances the correction policy at each iteration by incorporating knowledge gathered from previous iterations via data-driven confidence metrics assigned to prior corrections.

Address of the bookmark: https://github.com/NDBL/HECIL

Research Associate and JRF positions in the Structural and Computational Biology Group at ICGEB

Mon, 02 Feb 2015 23:00:37 -0600

Research Associate and JRF positions in the Structural and Computational Biology Group starting 1st March 2015. Collaborative projects include work on:

a) bioinformatics, systems and computational biology
b) malaria
c) drug discovery
d) genomics
e) microbiology
f) metabolic disorders
g) molecular medicine

Eligibility: Applicants must have one of the following :

1) INSPIRE award for undertakig either PhD or Postdoctoral research;
2) SPM award for PhD;
3) JRF for pursuing PhD from CSIR/DBT/ICMR

Interest and experience in Biochemistry/Bioinformatics/Biophysics/ Chemistry/Genomics/Molecular Biology/ is essential.

Submit curriculum vitae to sb.icgeb@gmail.com by 20 February 2015

Protocol for De novo Genome Assembly using Illumina Reads

BioStar — Sat, 16 Jan 2021 21:42:11 -0600

In this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.

What is de novo genome assembly?
The method of taking a large number of short DNA sequences and placing them back together to create a reflection of the original chromosomes from which the DNA originated relates to genome assembly. No previous knowledge of the source DNA sequence length, structure or composition is inferred by De novo genome assemblies. The DNA of the target organism is split up into millions of tiny parts and read on a sequencing computer in a genome sequencing experiment. Depending on the sequencing system used, these "reads" range from 20 to 1000 nucleotide base pairs (bp) in length. Usually, length reads of 36 - 150 bp are produced for Illumina style short read sequencing. These reads can be either “single ended” as described above or “paired end.”

Why genome assembly?
In basic research into why and how they live, as well as in applied topics, identifying the DNA sequence of an organism is useful. Awareness of a DNA sequence may be useful in virtually any biological research because of the relevance of DNA to living things. For example, it may be used in medicine to classify, diagnose and eventually improve genetic disorder therapies. Similarly, pathogens study can lead to treatments for infectious diseases.

Raw NGS data
Reads can be saved as a Fasta file as text or in a FastQ file with their attributes. FastQ is the most common read file format since this is what the Illumina sequencing pipeline creates. This will henceforth be the subject of our conversation.

In a nutshell the protocol:
Get the sequence file(s) read from the sequencing machine (s).
Look at the readings - have an idea of what you have and what the standard is like.
If required, raw data cleanup/quality trimming.
Choose an adequate parameter set for assembly.
Assemble the data into scaffolds/contigs.
Examine the assembly performance and determine the efficiency of the assembly.

Read Quality Control:
Check the qualiy with fastQC.
Script
https://bioinformaticsonline.com/snippets/view/42540/install-fastqc-using-conda

Quality trimming/cleanup of read files.
This function trims adapters, barcodes and other contaminants from the reads.
Script
https://bioinformaticsonline.com/snippets/view/42542/trimmomatic-command

Genome Assembly:
The object of this portion of the protocol is to explain the method of assembling the reads trimmed by quality into draft contigs.

spades.py -1 illumina_R1.fastq.gz -2 illumina_R2.fastq.gz --careful --cov-cutoff auto -o result_of_spades_assembly_all_illumina

A significant range of short-read assemblers are available. Everyone with strengths and disadvantages of their own.
Some of the assemblers available include:
Velvet
SOAP-denovo
MIRA
ALLPATHS

Next step is to assess the suitability and what to do with a draft package of contiguous details for the remainder of the study now. Few stuff you can note about the contigs you just created: They're the draft Contigs. Any mis-assemblies can occur.

Mis-assembly checking and assembly metric tools:
QUAST - Quality assessment tool for genome assembly http://bioinf.spbau.ru/quast
Mauve assembly metrics - http://code.google.com/p/ngopt/wiki/How_To_Score_Genome_Assemblies_with_Mauve
InGAP-SV - https://sites.google.com/site/nextgengenomics/ingap and http://ingap.sourceforge.net/
inGAP is also useful for finding structural variants between genomes from read mappings.

Genome finishing tools:
Semi-automated gap fillers:
Gap filler - http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/gapfiller/

IMAGE (V2) - http://sourceforge.net/apps/mediawiki/image2/index.php?title=Main_Page

Genome visualisers and editors:
Artemis - http://www.sanger.ac.uk/resources/software/artemis/
IGV - http://www.broadinstitute.org/igv/

Automated and semi automated annotation tools:
Prokka - https://github.com/tseemann/prokka
RAST - http://www.nmpdr.org/FIG/wiki/view.cgi/FIG/RapidAnnotationServer
JCVI Annotation Service - http://www.jcvi.org/cms/research/projects/annotation-service/

Frequent command use for the analysis are at:

https://bioinformaticsonline.com/blog/view/38765/list-of-tools-frequently-used-while-genome-assembly
https://bioinformaticsonline.com/pages/view/42275/frequent-parameters-for-bioinformatics-tools

JRF / Project Assistant Recruitment at Shillong – Bioinformatics Centre (DIC)

Sat, 07 Feb 2015 06:00:23 -0600

3 Vacancies at Bioinformatics Centre (DIC) For M.Tech/M.Sc. Degree Candidates. Apply Before 15th February,2015

Bioinformatics Centre (DIC) invites applications for the following posts:

Job Number: 01
Job Designation: Junior Research Fellow (JRF)
Number of Vacancy: 02 (Two)
Educational Qualification:
M.Tech/M.Sc. in Life Sciences/Botany/Zoology/Biochemistry/Biotechnology/Bioinformatics.
Desirable Qualification:
Aptitude for Bioinformatics and Computer Programming/Next generation sequencing data analysis.

Job Number: 02
Job Designation: Project Assistant
Number of Vacancy: 01 (One)
Educational Qualification:
Graduation in Science.
Desirable Qualification:
Experience of working in a Life Science/Plant Biotechnology Lab.

Place of Work: Shillong

How To Apply For Opening:
The applications through email bicnehu@gmail.com or post must reach the undersigned within 15 days from the date of publication of this advertisement.

Last Date To Apply: 15th February,2015

Contact Address: Bioinformatics Centre (DIC),Shillong-793022

Advertisement Details: Employment News (31 January – 6 February) Page 28

GView: A Java application for viewing and examining prokaryotic genomes in a circular or linear context

Abhimanyu Singh — Fri, 14 Jul 2017 07:47:03 -0500

GView is a Java application for viewing and examining prokaryotic genomes in a circular or linear context. It accepts standard sequence file formats and an optional style specification file to generate customizable, publication quality genome maps in bitmap and scalable vector graphics formats. GView features an interactive pan-and-zoom interface, a command-line interface for incorporation in genome analysis pipelines, and a public Application Programming Interface for incorporation in other Java applications.

Availability: GView is a freely available application licensed under the GNU Public License. The application, source code, documentation, file specifications, tutorials and image galleries are available at http://gview.ca

Contact: ac.cg.cpsa-cahp@raalesmod.nav.yrag

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995121/

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995121/

Bioinformatics PhDs - Cover Letter

Martin Jones — Mon, 16 Feb 2015 12:48:52 -0600

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.

I-PV: Interactive Protein Sequence Visualization

Jit — Mon, 03 Jul 2017 07:52:51 -0500

I-PV is a interactive data visualization software designed for inspection of protein sequences and mutation information. It is mainly used for Genetics and Bioinformatics. So what exactly makes it standout?

http://i-pv.org/ipv_rec

Address of the bookmark: http://i-pv.org/

R for Microsoft Excel

Jitendra Narayan — Wed, 18 Feb 2015 00:43:27 -0600

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/