BOL

proActiv is an R package that estimates promoter activity from RNA-Seq data. proActiv uses aligned reads and genome annotations as input, and provides absolute and relative promoter activity as output. The package can be used to identify active...

PyParanoid is a pipeline for rapid identification of homologous gene families in a set of genomes - a central task of any comparative genomics analysis. The "gold standard" for identifying homologs is to use reciprocal best hits (RBHs) which depends...

kallisto can process either single-end or paired-end reads. The default running mode is paired-end and requires an even number of FASTQ files represented as pairs, e.g. kallisto quant -i index -o output pairA_1.fastq pairA_2.fastq...

PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for...

SEASTAR (Systematic Evaluation of Alternative STArt site in RNA) is a software package for Transcription Start Site (TSS) identification and quantification using only RNA-seq data. It assembles novel TSSs based only on RNA-Seq data and merges them...

Omics Teaching materials- https://github.com/hbctraining #Omics #tutorials #Scripts

International Journal of Bioinformatics Research and Applications Indexed in  Scopus (Elsevier) Academic OneFile (Gale) ACM Digital Library Current Awareness in Biological Sciences (Elsevier) Chemical Abstracts (CAS)

ENCODE 3 A collection of research articles and related content describing the Encyclopedia of DNA Elements, its datasets and tools.

GROMACS is a versatile package to perform molecular dynamics, i.e simulate the Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is able to work with many biochemical molecules like proteins, lipids and...

The PheWAS R package is designed to provide an accessible interface to the phenome wide association study. For a description of the methods available and some simple examples, please see the package vignette or the R documentation. For...

To know the entire python version. $ conda search "^python$" #Search #Python #Version

#To install perl modules perl -MCPAN -e shell # go to CPAN install modeinstall Bundle::CPAN # update CPANreload cpaninstall Set::Scalar

Common one-liner for bioinformatician !

WGDdetector pipeline that integrates all analyses including gene family constructing, dS estimating and phasing, and outputting the dS values of each paralogs pairs processed with only one command. We further chose four species (Arabidopsis...