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process-featurecounts

Process and simplify featureCounts output files

progressivecactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules

qtl

R/qtl: A QTL mapping environment

qtl2

QTL analysis software for high-dimensional data and complex cross designs

qtlcharts

R/qtlcharts: An R package for interactive QTL graphics

quast

Genome assembly evaluation tool

radscan

A utility for performing domain architecture-based protein similarity search (using RADS/RAMPAGE).

randomperlscripts

Random Perl scripts to do a variety of things

rcombinator

An R/C++ package for simulating the evolution of retrotransposons over time.

reannte

Scripts to help transposable elements consensus sequences curation

repclass

This tool facilitates transposable elements consensus classification

ripgrep

ripgrep recursively searches directories for a regex pattern

ripgrep-all

rga: ripgrep, but also search in PDFs, E-Books, Office documents, zip, tar.gz, etc.

rna-seq-analysis

RNAseq analysis notes from Ming Tang

rna-seq_tccomp

Comparison of RNA-seq time course differential expression analysis tools

rnaseq

RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

salsa

SALSA: A tool to scaffold long read assemblies with Hi-C data

satsuma2

FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing

scbatch

Batch Effect Correction of RNA-seq Data through Sample Distance Matrix Adjustment

scbatch-paper-scripts

Scripts used to generate Figs. 2-5 in scBatch manuscript

seqan

SeqAn's official repository.

seqplots

:chart_with_upwards_trend:SeqPlots - An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.

seqtk

Toolkit for processing sequences in FASTA/Q formats

shasta

De novo assembly from Oxford Nanopore reads.

shinychromosome

an R/Shiny application for interactive creation of non-circular plots of whole genomes

shinycircos

an R/shiny application for creation of Circos plot interactively

sibeliaz

sift-seq

Using deep learning to identify whether short sequences of DNA are viral, human, or bacterial in origin

softsearch