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latch
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public |
The Latch python bioinformatics framework
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2025-04-21 |
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usalign
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public |
Universal structure alignment of monomeric, complex proteins and nucleic acids
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2025-04-21 |
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maxit
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public |
MAXIT assists in the processing and curation of macromolecular structure data.
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2025-04-21 |
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strangepg
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public |
Strange pangenome-scale interactive graph visualizer
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2025-04-21 |
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iow
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public |
Implementation of Balanced Parentheses
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2025-04-21 |
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unifrac
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public |
Fast phylogenetic diversity calculations
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2025-04-21 |
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jbrowse2
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public |
The JBrowse 2 Genome Browser
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2025-04-21 |
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ucsc-cell-browser
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public |
A browser for single-cell data, main site at http://cells.ucsc.edu. UCSC Cellbrowser, an interactive browser for single cell data. Includes importers and basic pipelines for text files, Seurat, Scanpy and Cellranger. All Javascript - does not require a server backend.
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2025-04-21 |
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r-pscbs
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public |
Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
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2025-04-21 |
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ncbi-datasets-pyclient
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public |
NCBI Datasets API
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2025-04-21 |
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perl-mime-types
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public |
Definition of MIME types
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2025-04-21 |
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oakvar
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public |
OakVar - Genomic Variant Analysis Platform
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2025-04-21 |
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argnorm
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public |
Normalize antibiotic resistance genes (ARGs) abundance tables (e.g., from metagenomics) by using the ARO ontology (developed by CARD).
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2025-04-21 |
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pmultiqc
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public |
Python package for quality control of proteomics datasets, based on multiqc package
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2025-04-20 |
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quantms-utils
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public |
Python package with scripts and helpers for the quantms workflow.
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2025-04-20 |
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pytantan
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public |
Cython bindings and Python interface to Tantan, a fast method for identifying repeats in DNA and protein sequences.
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2025-04-19 |
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needletail
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public |
Fast FASTX parsing in Python
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2025-04-19 |
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mappy
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public |
Minimap2 Python binding
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2025-04-18 |
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miniprot
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public |
Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift.
It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.
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2025-04-18 |
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minimap2
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public |
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
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2025-04-18 |
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pybiolib
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public |
BioLib Python Client
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2025-04-18 |
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pilea
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public |
Pilea: profiling bacterial growth dynamics from metagenomes with sketching
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2025-04-18 |
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mimick
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public |
Simulate linked-read data.
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2025-04-18 |
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stripepy-hic
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public |
StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning
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2025-04-18 |
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esme_pnetcdf_mvapich_4_0
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public |
PnetCDF - Parallel netCDF
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2025-04-18 |
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esme_esmf_mvapich_4_0
|
public |
ESMF - Earth System Modeling Framework
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2025-04-18 |
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esme_mvapich_4_0
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public |
Earth System Modelling Environment (ESME) - A bundle for scientific computing packages for climate modelling with MPI support.
|
2025-04-18 |
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esme_netcdf-fortran_mvapich_4_0
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public |
NetCDF-Fortran - netCDF interface for Fortran
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2025-04-18 |
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esme_netcdf-c_mvapich_4_0
|
public |
NetCDF-C - netCDF interface for C
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2025-04-18 |
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esme_pio_mvapich_4_0
|
public |
ParallelIO - High-level parallel I/O library
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2025-04-18 |
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esme_hdf5_mvapich_4_0
|
public |
HDF5 - Hierarchical Data Format 5
|
2025-04-18 |
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esme_omb_mvapich_4_0
|
public |
OSU Micro Benchmarks
|
2025-04-18 |
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sentieon
|
public |
Accelerated performance bioinformatics tools for mapping and variant calling
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2025-04-18 |
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hictkpy
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public |
Python bindings for hictk: read and write .cool and .hic files directly from Python
|
2025-04-18 |
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diamond
|
public |
Accelerated BLAST compatible local sequence aligner.
|
2025-04-18 |
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rgi
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public |
This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website
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2025-04-18 |
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emboss
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public |
The European Molecular Biology Open Software Suite
|
2025-04-18 |
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gtdbtk
|
public |
A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
|
2025-04-18 |
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msoma
|
public |
mSOMA: Somatic Mutation Detection using a betabinomial null model
|
2025-04-18 |
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mgnify-pipelines-toolkit
|
public |
Collection of scripts and tools for MGnify pipelines.
|
2025-04-18 |
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codingquarry
|
public |
CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts.
|
2025-04-18 |
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squirrel
|
public |
Some QUIck Reconstruction to Resolve Evolutionary Links
|
2025-04-18 |
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hmftools-chord
|
public |
Predict HRD using somatic mutations contexts
|
2025-04-18 |
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perl-io-interactive
|
public |
Utilities for interactive I/O
|
2025-04-18 |
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vuegen
|
public |
VueGen automates the creation of reports from bioinformatics outputs,
supporting formats like PDF, HTML, DOCX, ODT, PPTX, Reveal.js,
Jupyter notebooks, and Streamlit web applications. Users simply
provide a directory with output files—such as plots, tables, networks,
Markdown text, and HTML files—and VueGen compiles them into a structured report.
|
2025-04-18 |
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rdrpcatch
|
public |
RNA virus RdRp sequence scanner.
|
2025-04-18 |
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vcfdist
|
public |
vcfdist: benchmarking phased germline variant calls in VCF format
|
2025-04-18 |
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gemma
|
public |
Linear mixed models (LMMs) for genome-wide association (GWA)
|
2025-04-18 |
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gadma
|
public |
Genetic Algorithm for Demographic Inference
|
2025-04-18 |
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flair
|
public |
Correction, isoform definition, and alternative splicing analysis of noisy reads (ONT and PacBio).
|
2025-04-18 |
