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ariang

AriaNg, support aria2c command-line-like

bamutil

batch-effect-removal-benchmarking

A benchmark of batch-effect correction methods for single-cell RNA sequencing data

bedtools2

A powerful toolset for genome arithmetic.

bsseq

Devel repository for bsseq

bwa-docker

Minimal docker image for bwa

cas-analyzer

Full JavaScript-based assessment tool for targeted sequencing data of genome-edited samples.

cellranger

10x Genomics Single Cell 3' Gene Expression and VDJ Assembly

cellxgene_vip

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

deepbind-with-pytorch

CNN architecture for predicting DNA binding sites for Transcription Factors

deeptools

Tools to process and analyze deep sequencing data.

drugvqa

Predicting Drug Protein Interaction using Quasi-Visual Question Answering System

easy_af2

Easy to AF2

egui

gene_lists

List of gene lists for genomic analyses.

geograpy

Extract countries, regions and cities from a URL or text

ggalluvial

Shiny only for https://github.com/corybrunson/ggalluvial

good.software

This project contains the links to the datasets, and code that was used for our study "Software crisis in computational biology? Towards a better usability and archival stability of bioinformatics software"

how_are_we_stranded_here

Check strandedness of RNA-Seq fastq files

igv.js

Lightweight html5 version of the Integrative Genomics Viewer

interactivecomplexheatmap

Make Interactive Complex Heatmaps

intervene-shiny

An interactive Shiny App for UpSet plots, Venn diagrams and Pairwise heatmaps

lago

Open Source Metering and Usage Based Billing

lamarck

mavr

various bioinformatic instruments

mind2mm

Simple tool, that convert mindmester.com files to FreeMind format

nucit

Automatically exported from code.google.com/p/nucit

nucleoatac

nucleosome calling using ATAC-seq

panel

Panel: The powerful data exploration & web app framework for Python

pantera

Protein-coding gene prediction tool