PyaniPython module for average nucleotide identity analyses
Stars: ✭ 111 (-26.49%)
PymzmlpymzML - an interface between Python and mzML Mass spectrometry Files
Stars: ✭ 100 (-33.77%)
DeepecgECG classification programs based on ML/DL methods
Stars: ✭ 124 (-17.88%)
Bio4jBio4j abstract model and general entry point to the project
Stars: ✭ 113 (-25.17%)
RiddleRace and ethnicity Imputation from Disease history with Deep LEarning
Stars: ✭ 91 (-39.74%)
SortmernaSortMeRNA: next-generation sequence filtering and alignment tool
Stars: ✭ 108 (-28.48%)
HifiasmHifiasm: a haplotype-resolved assembler for accurate Hifi reads
Stars: ✭ 134 (-11.26%)
Dnachisel✏️ A versatile DNA sequence optimizer
Stars: ✭ 95 (-37.09%)
CirclatorA tool to circularize genome assemblies
Stars: ✭ 121 (-19.87%)
CoolerA cool place to store your Hi-C
Stars: ✭ 112 (-25.83%)
MolgenisMOLGENIS - for scientific data: management, exploration, integration and analysis.
Stars: ✭ 88 (-41.72%)
ReadfqFast multi-line FASTA/Q reader in several programming languages
Stars: ✭ 128 (-15.23%)
BioconvertBioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
Stars: ✭ 112 (-25.83%)
HgvsPython library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Stars: ✭ 138 (-8.61%)
PegasusPegasus Workflow Management System - Automate, recover, and debug scientific computations.
Stars: ✭ 110 (-27.15%)
PlipProtein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315
Stars: ✭ 123 (-18.54%)
BedtkA simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
Stars: ✭ 103 (-31.79%)
KaijuFast taxonomic classification of metagenomic sequencing reads using a protein reference database
Stars: ✭ 146 (-3.31%)
BionitioDemonstrating best practices for bioinformatics command line tools
Stars: ✭ 97 (-35.76%)
Kmer CntCode examples of fast and simple k-mer counters for tutorial purposes
Stars: ✭ 124 (-17.88%)
OctopusBayesian haplotype-based mutation calling
Stars: ✭ 131 (-13.25%)
HicexplorerHiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
Stars: ✭ 116 (-23.18%)
Apbs Pdb2pqrAPBS - software for biomolecular electrostatics and solvation
Stars: ✭ 114 (-24.5%)
DecontamSimple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Stars: ✭ 86 (-43.05%)
Hts Nimnim wrapper for htslib for parsing genomics data files
Stars: ✭ 132 (-12.58%)
FqtoolsAn efficient FASTQ manipulation suite
Stars: ✭ 114 (-24.5%)
UgeneUGENE is free open-source cross-platform bioinformatics software
Stars: ✭ 112 (-25.83%)
SplatterSimple simulation of single-cell RNA sequencing data
Stars: ✭ 128 (-15.23%)
BiofastBenchmarking programming languages/implementations for common tasks in Bioinformatics
Stars: ✭ 112 (-25.83%)
ScdeR package for analyzing single-cell RNA-seq data
Stars: ✭ 147 (-2.65%)
CgrangesA C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
Stars: ✭ 111 (-26.49%)
Somalierfast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Stars: ✭ 128 (-15.23%)
TaxonkitA Practical and Efficient NCBI Taxonomy Toolkit
Stars: ✭ 109 (-27.81%)
ArtemisArtemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
Stars: ✭ 135 (-10.6%)
IndraINDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
Stars: ✭ 105 (-30.46%)
SarekDetect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
Stars: ✭ 124 (-17.88%)
GenomicsA collection of scripts and notes related to genomics and bioinformatics
Stars: ✭ 101 (-33.11%)
Soapdenovo2Next generation sequencing reads de novo assembler.
Stars: ✭ 150 (-0.66%)
SmudgeplotInference of ploidy and heterozygosity structure using whole genome sequencing data
Stars: ✭ 98 (-35.1%)
Krakenuniq🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
Stars: ✭ 123 (-18.54%)
AribaAntimicrobial Resistance Identification By Assembly
Stars: ✭ 96 (-36.42%)
Awesome Single CellCommunity-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Stars: ✭ 1,937 (+1182.78%)
NextflowA DSL for data-driven computational pipelines
Stars: ✭ 1,337 (+785.43%)
ScgenSingle cell perturbation prediction
Stars: ✭ 122 (-19.21%)
FastqtFastQC port to Qt5: A quality control tool for high throughput sequence data.
Stars: ✭ 92 (-39.07%)
PysradbPackage for fetching metadata and downloading data from SRA/ENA/GEO
Stars: ✭ 146 (-3.31%)
BioBioinformatics library for .NET
Stars: ✭ 90 (-40.4%)
BlacklistApplication for making ENCODE Blacklists
Stars: ✭ 119 (-21.19%)
SwarmA robust and fast clustering method for amplicon-based studies
Stars: ✭ 88 (-41.72%)
MrbayesMrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:
Stars: ✭ 131 (-13.25%)
Dna2vecdna2vec: Consistent vector representations of variable-length k-mers
Stars: ✭ 117 (-22.52%)
BiograknBioGrakn Knowledge Graph
Stars: ✭ 152 (+0.66%)
MixcrMiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.
Stars: ✭ 148 (-1.99%)
BiotiteA comprehensive library for computational molecular biology
Stars: ✭ 132 (-12.58%)
NglessNGLess: NGS with less work
Stars: ✭ 115 (-23.84%)