bioinformatics
Repositories (1466)
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...
โ๏ธ 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
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
๐๐๐ฎ๐ก๐ค๐๐๐ฃ๐๐ฉ๐๐ ๐พ๐ค๐ข๐ฅ๐ค๐ฃ๐๐ฃ๐ฉ ๐๐ง๐๐ฅ๐ โธบ 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
๐งฌ 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.
netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation
viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data
A collection of publications on comparison of high-throughput sequencing technologies.
DeepSEA in TensorFlow
Software packages for smart growing environments.
DriverPower
An R package for reproducible and automated ADMIXTOOLS analyses
The BridgeDb Library source code
Toolkit for preparing genomes for submission to NCBI
A collection of resources to filter 'bad' probes from the Illumina 450k and EPIC methylation arrays
Some useful python scripts for biologists
A Python package for drug discovery by analyzing causal paths on multiscale networks
APBS & PDB2PQR - software for biomolecular electrostatics and solvation
Collection of YouTube videos on data science on the Data Professor YouTube channel.
Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples
Materials for the Training and Engagement Website
A tool for projecting genomic alignments to transcriptomic coordinates
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that cons...
Zavolan-Lab Automated RNA-Seq Pipeline
Synthetic lethality (SL) is a promising gold mine for the discovery of anti-cancer drug targets. KG4SL is the first graph neural network (GNN)-based m...