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py-macs3 Peak caller aimed at transcription factor binding sites
py-mappy (V) Minimap2 python binding
py-mdanalysis (V) Library to analyze and manipulate molecular dynamics trajectories
py-mdtraj (V) The analysis of molecular dynamics trajectories
py-mmLib (V) Python Macromolecular Library
py-multiqc Aggregate bioinformatics analysis reports across samples and tools
py-neo (V) Python package for representing electrophysiology data
py-nibabel (V) Access a multitude of neuroimaging data formats
py-nilearn (V) Statistical learning for neuroimaging in Python
py-prody (V) Python Package for Protein Dynamics Analysis
py-psychopy (V) Psychology and neuroscience software in python
py-pydeseq2 (V) Python implementation of the popular DESeq2 R package
py-pydicom Pure python package for working with DICOM files
py-pygr (V) Pygr graph database for bioinformatics
py-pyquante (V) Quantum chemistry in Python
py-pysam (V) Python module for reading, manipulating and writing genomic data sets
py-pysb (V) Python Systems Biology modeling framework
py-spglib (V) Python bindings for finding and handling crystal symmetries
py-sumatra (V) Tracking projects based on numerical simulation or analysis
py-thermo (V) Chemical properties component of ChEDL
py-thermopy (V) Some utilities for Thermodynamics and Thermochemistry
py-varify (V) Clinical DNA Sequencing Analysis and Data Discovery
R-popbio Construction and Analysis of Matrix Population Models
R-rgbif (V) Interface to the Global Biodiversity Information Facility API
racon Genomic consensus builder
rasmol Molecular Graphics Visualisation Tool
readseq (V) Read and reformat biosequences, Java command-line version
rna-seq Core tools needed for RNA-Seq analysis
rna-star Spliced Transcripts Alignment to a Reference
samtools Tools for manipulating sequence alignment maps
seqtk Tool for processing sequences in FASTA/FASTQ format
sewer SEquence Analysis using WEb Resources
sra-tools NCBI's toolkit for handling data in INSDC Sequence Read Archives
stacks Software pipeline for building loci from short-read sequences
stride Protein secondary structure assignment from atomic coordinates
stringtie Transcript assembly and quantification for RNA-seq
subread High-performance read alignment, quantification and mutation discovery
trimmomatic Flexible read trimming tool for Illumina NGS data
vcf-split Split a multi-sample VCF into single-sample VCFs
vcf2hap Generate .hap file from VCF for haplohseq
vsearch Versatile open-source tool for metagenomics
xmakemol Program for visualizing atomic and molecular systems
xylem Tools for manipulation of genetic databases