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 .

https://www.hindawi.com/journals/ijpg/2011/373875/

Address of the bookmark: https://sourceforge.net/projects/cvit/

Qualification : Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application/ Life Science/ Biotechnology/ Agricultural Science or equivalent. Desirable: Knowledge of Statistical and Computational Genomics/ Proteomics/ Bioinformatics OR Post-Graduation in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application/ Life Science/ Biotechnology/ Agricultural Science or equivalent with 1st Division or 60% marks or equivalent with at least two years of research experience. Desirable:Expertise on use of various software/ tool.

No.of Post: 2

Emoluments for RA: Consolidated Rs. 24000/- per month + 30% HRA for Ph.D holders and consolidated Rs. 23000/- per month + 30% HRA for Master Degree.

Age Limit : Age should not be more than 40 years for the post of Research associate (5 years relaxation for SC/ST/ women candidates) and 3 years for OBC candidates as on date of interview.
How to apply

Interested candidates are invited to appear for Walk-In interview at Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi -110012, along with filled in application form , all the original certificates from matriculation onwards, Ph.D. or M.Sc. certificate (as the case may be) must be produced at the time of interview in either original or provisional, Bio-Data, attested copies of all experience certificates, testimonials etc., one passport size photograph and one set of the self-attested photocopies of all the required certificates from matriculation onwards and an attested copy of recent passport size photograph pasted onto the application form. Walk-in interview will be held on 16th April, 2015 at 10:30 a.m.

Click Here for Job Details & Application Form http://www.iasri.res.in/employment/employment.htm

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/QuasR/inst/doc/QuasR.html

Bioinformatics is full of opportunities. The sector is poised to open new avenues for the other related sectors also. But the biggest opportunity area in the Bioinformatics market will be in the drug discovery sector. Reduction of both the cost and time taken to discover a new drug due to fast development in the Bioinformatics tools and software zone is also making drug discovery an attractive field to venture in. Malaysian bioinformatics growth and future are discuss in this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723929/ paper. Keeping all such inportance in mind, following universities in Malaysia offering bioinformatics cources:

3 program(s) at AIMST University, Malaysia

Master of Science in Biotechnology (MSc) - Bioinformatics by Research

Master of Science (M.Sc) in Medical Microbiology (Bioinformatics) by Research

Doctor of Philosophy in Biotechnology (PhD) - Bioinformatics by Research

1 program(s) at INTI International University and Colleges, Malaysia

American Degree Transfer Program (Biosciences) in Bioinformatics

3 program(s) at Management and Science University (MSU), Malaysia

Master in Bioinformatics (By Research)

PhD in Bioinformatics

Bachelor in Bioinformatics (Hons)

1 program(s) at Multimedia University (MMU), Malaysia

Bachelor of Science (Honours) Bioinformatics

1 program(s) at Universiti Industri Selangor (UNISEL) Bestari Jaya Campus, Malaysia

Bachelor of Bioinformatics (Hons)

2 program(s) at Universiti Malaysia Sabah (UMS), Malaysia

PhD - Doctor of Philosophy in Bioinformatics (By Research)

MSc - Master of Science in Bioinformatics (By Research)

6 program(s) at Universiti Putra Malaysia (UPM), Malaysia

MSc - Master of Science in Bioinformatics by Research

Master of Science in Bioinformatics and System Biology by Research

Master of Science (M.Sc) in Bioinformatics and Systems Biology (With Thesis)

PhD - Doctor of Philosophy in Bioinformatics by Research

PhD - Doctor of Philosophy in Bioinformatics and Systems Biology (With Thesis)

PhD - Doctor of Philosophy in Bioinformatics and System Biology by Research

1 program(s) at Universiti Selangor (UNISEL), Malaysia

Bachelor of Bioinformatics (Hons)

3 program(s) at Universiti Teknologi Malaysia (UTM), Malaysia

M.Sc - Master of Science (Bioscience) in Bioinformatics Research Group (BIRG) By Research

PhD - Doctor of Philosophy (Bioscience) in Bioinformatics Research Group (BIRG) By Research

Bachelor of Computer Science (BioInformatics)

4 program(s) at University of Malaya (UM), Malaysia

MSc - Master of Science in Bioinformatics by Research

Master in Bioinformatics by Coursework

PhD - Doctor of Philosophy in Bioinformatics by Research

Bachelor of Science (BSc) in Bioinformatics

3 program(s) at Perdana University, Malaysia

Master in Bioinformatics (By Research)

PhD in Bioinformatics

Bachelor in Bioinformatics (Hons)

3 program(s) at Monash University, Malaysia

Master in Bioinformatics (By Research)

PhD in Bioinformatics

Bachelor in Bioinformatics (Hons)

The real bioinformatics scope lies if there are research labs which work in this field. One has to take account of that. If so then try to get information of those labs and visit them to get a hang of the work they pursue. For detail Bioinformatics in Malaysia: Hope, Initiative, Effort, Reality, and Challenges are discussed in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723929/ paper.

FIGENO is a
  FIGure
    GENerator
for GENOmics

With figeno, you can plot various types of sequencing data along genomic coordinates. Video overview: https://www.youtube.com/watch?v=h1cBeXoSYTA.

Address of the bookmark: https://github.com/CompEpigen/figeno

Candidates desirous of doing a short-term training / final year dissertation project for MSc (Life Sciences/Bioinformatics/Biotechnology or any science discipline) at UIAR Biophysics and Bioinformatics department may please drop an email atanju@iiar.res.in along with their resume.

Selected candidates will be further intimated. There will be a fees charged for doing the project at UIAR. The projects will be experimental or computational or involve both.

The training scope will be in the following areas but not limited to:

Bioinformatics analysis, Docking and Virtual screening, Molecular Dynamics simulation, Cloning, expression and purification of proteins, Biophysical and Biochemical characterisation of proteins, Crystallization and Structural Studies.

Advertisement: www.iiar.res.in/?q=node/450

To tackle this problem, researchers developed a new bioinformatics tool called ntSynt. It was first introduced in a 2025 study in BMC Biology titled “ntSynt: multi-genome synteny detection using minimizer graph mappings”. This tool (https://github.com/BirolLab/ntSynt) helps researcher find conserved genomic regions across several species without relying on traditional whole-genome alignments or gene annotations. Instead, ntSynt uses short DNA sequences called minimizers as landmarks. It finds minimizers shared by different genomes and maps their relationships in a graph, making it possible to spot large genomic regions that have kept a similar structure over time. The tool uses Bloom filters and graph-based mapping, which lets scientists analyze many genomes at once while saving memory and processing time.

The team tested ntSynt using both simulated data and real genomic sequences from groups like humans, chimpanzees, bonobos, gorillas, rodents, and bees. Their results showed that ntSynt can find conserved genomic regions and spot structural differences between species. In simulated tests, ntSynt identified syntenic blocks with over 97% accuracy. One standout example involved eleven bee genomes from the genus Andrena, which have a lot of variation in chromosome organization. Despite these differences, ntSynt found conserved regions covering about 85% of the smallest bee genome, completing the analysis in just 14.7 minutes and using less than 4 GB of memory. These findings highlight ntSynt’s potential for large-scale comparative genomics, where efficiency is crucial as more genomes become available.

An interesting result came up when the researchers compared primate genomes. When they looked at regions conserved between humans and other great apes, ntSynt flagged what looked like a large deletion in one gorilla genome assembly. After checking with long-read sequencing data, they found that the missing section was likely a mistake in the assembly, not a real evolutionary change. This means ntSynt can help not only with studying evolutionary relationships but also with spotting possible errors in genome assemblies. By highlighting unexpected breaks in regions that are usually conserved, the tool helps scientists tell apart true evolutionary changes from technical mistakes in reference sequences.

The importance of ntSynt becomes even clearer when we look at global projects to sequence and study Earth’s biodiversity. Projects like the Earth BioGenome Project aim to create genomic resources for many different organisms, opening up new ways to explore the history of life. But generating genomic data is just the beginning; making sense of these relationships requires powerful and scalable tools. ntSynt helps by letting researchers study chromosome evolution, conserved genome structures, and rearrangements across many species. While the tool has some limits, especially with detecting duplicated regions or analyzing very different genomes, its speed and scalability make it a valuable tool for modern comparative genomics.

The creation of ntSynt marks a significant advancement in our understanding of how genomes have evolved and become diverse over Earth's history. Since each conserved region in the genome is evidence of common ancestry and each rearrangement gives hinThe development of ntSynt is a big step forward in understanding how genomes have changed and diversified over time. Each conserved region in a genome points to shared ancestry, and each rearrangement offers clues about evolutionary events in different lineages. ntSynt helps scientists spot these patterns more easily, opening up new ways to study genome evolution across the tree of life. Evolution’s story isn’t just in the DNA sequence, but also in how those sequences are arranged and preserved over millions of years. Tools like ntSynt are helping scientists read this hidden story more clearly and reveal the deep genomic connections that link all life on Earth.

More at https://link.springer.com/article/10.1186/s12915-025-02455-w?

Job Description

• Work within a fast-paced, collaborative environment with small project teams working on a variety of tasks ranging from new product development to DNA data processing
• Collaborate with Centrillion research scientists in order to bridge the gap between the laboratory and the digital world
• Develop tools to enable research projects to cope with the enormous amounts of data produced by modern DNA sequencing experiments
• Build simulation algorithms to help guide and analyze research done in the lab
• Solve challenging engineering problems that require the development of innovative algorithms

Requirements

• Strong background in mathematics/statistics with a degree in a related field
• Strong analytical, coding, communication, and organizational skills
• Experience with algorithm development, simulations, and data analysis
• Proficiency in at least one modern programming language (like Python or Perl)
• Experience analyzing genetic and biological data sets (e.g., DNA data analysis and image analysis)
• Experience with machine learning and pattern recognition is preferred

Please submit your resume at https://www.centrillionbio.com/career/ to apply for this position.

Copy & Paste this line into your terminal:

\curl -L https://install.perlbrew.pl | bash

Or, if your system does not have curl but something else:

# Linux
\wget -O - https://install.perlbrew.pl | bash

# FreeBSD
\fetch -o- https://install.perlbrew.pl | sh

If you prefer to install with cpan, there are two steps:

sudo cpan App::perlbrew
perlbrew init

If it is installed with cpan, the perlbrew executable should be installed as /usr/bin/perlbrew or /usr/local/bin/perlbrew. For all users who want to use perlbrew, a prior perlbrew init needs to be executed.

The default perlbrew root directory is ~/perl5/perlbrew, which can be changed by setting PERLBREW_ROOTenvironment variable before the installation and initialization. For more advanced installation process, please read the perlbrew document.

Address of the bookmark: https://perlbrew.pl/