bioinformatics

Interpretable genotype-phenotype landscape modeling

:bookmark: Get SNP proxies from the 1000 Genomes Project.

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Tools for querying and analysis of genomic data

BigWig manpulation tools using libBigWig and htslib

This repository contains course materials from JAX-BD2K workshop.

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

(formerly eelpond) an automated RNA-Seq workflow system

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

The official PySCeS project source code repository.

A phylogenetic profile analysis tool

A Python package for gene network analysis

Nucleic and amino acid primitive types

Genetic Heterogeneity Profiling by Single Cell RNA Sequencing

ASAP : Automated Single-cell Analysis Pipeline

Identify phage regions in bacterial genomes for masking purposes

R package for High dimensional data analysis and integration with O2PLS!

Workshop • Analysis of RNA-seq data

An R package to plot interactive three-way differential expression analysis

A Python package to calculate, visualize and analyze correlation maps of proteins.

The script presents a simple way to visualize features on human chromosome ideograms

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

Repository of our application for human-augmented binning

creating hybrid-gene phylogenetic trees for diversity analyses

Bioconnector Workshops

Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny amo...

⚙️ A lightweight immune repertoire browser

An information-theoretic pipeline for methylation analysis of WGBS data

Predicting regulatory DNA elements based on epigenomic signatures

Taxon-aware analysis of clustered protein sequences

An automatic classification tool for PVS1 interpretation of null variants

Create WDL documentation using Markdown.

Super snazzy online phylogenetic tree viewer with automatic customization using simple, tab-separated text files.

A project for exploring differentially active signaling paths related to proteomics datasets

Python Implementation of Codon Adaption Index

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

ntHash implementation in Rust

A tool for accurately detecting actively translating ORFs from Ribo-seq data

AutoImpute : Autoencoder based imputation of single cell RNA-seq data

Deep learning for Metagenome Assembly Error Detection

🧬 MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations

(No maintenance) Detect gene fusion directly from raw fastq files

A client for the Ensembl REST API written in the Python programming language

Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)

transparently build CWL and Galaxy XML tool definitions for any script that uses argparse

Open source Java library for computational proteomics

RNAcentral website source code

:bug: How to use CENTIPEDE to determine if a transcription factor is bound.