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galaxy-files
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public |
The Galaxy file sources framework and default plugins.
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2025-03-08 |
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galaxy-objectstore
|
public |
The Galaxy object store framework and default implementations
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2025-03-08 |
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galaxy-schema
|
public |
The Galaxy API schema objects.
|
2025-03-08 |
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postmaster
|
public |
Postmaster is a tool for annotating transcriptome alignments with posterior alignment probabilities derived from salmon quantifications.
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2025-03-08 |
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danbing-tk
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public |
Toolkit for VNTR genotyping and repeat-pan genome graph construction
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2025-03-08 |
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longbow
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public |
A Python program for nanopore sequencing basecalling configuration prediction
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2025-03-08 |
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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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2025-03-08 |
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last
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public |
LAST finds & aligns related regions of sequences.
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2025-03-07 |
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gmap
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public |
Genomic mapping and alignment program for mRNA and EST sequences.
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2025-03-07 |
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callingcardstools
|
public |
An API and collection of cmd line tools to work with calling cards sequencing data
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2025-03-07 |
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taxtastic
|
public |
Tools for taxonomic naming and annotation
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2025-03-07 |
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r-signac
|
public |
A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart and Butler et al. (2019) <doi:10.1016/j.cell.2019.05.031>.
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2025-03-07 |
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cctk
|
public |
Tools to identify and compare CRISPR arrays.
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2025-03-07 |
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r-psminer
|
public |
Utilities for interacting with the pathogensurveillance pipeline.
|
2025-03-07 |
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busco
|
public |
Assessment of assembly completeness using Universal Single Copy Orthologs.
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2025-03-07 |
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omark
|
public |
OMArk - Proteome quality assesment based on OMAmer placements
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2025-03-07 |
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perl-bio-phylo-forest-dbtree
|
public |
DBIx::Class-backed, Bio::Phylo-like API for large phylogenies.
|
2025-03-07 |
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wfmash
|
public |
a pangenome-scale aligner
|
2025-03-07 |
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te-aid
|
public |
Annotation helper tool for the manual curation of transposable element consensus sequences
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2025-03-07 |
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bioblend
|
public |
A Python library for interacting with the Galaxy API.
|
2025-03-07 |
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hmftools-cuppa
|
public |
Predict tissue of origin for tumor samples from WGTS data.
|
2025-03-07 |
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pegas
|
public |
PeGAS is a Snakemake pipeline for genome analysis
|
2025-03-07 |
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lassaseq
|
public |
Tool for downloading Lassa virus sequences
|
2025-03-07 |
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snakemake-executor-plugin-kubernetes
|
public |
A snakemake executor plugin for submission of jobs to Kubernetes
|
2025-03-07 |
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ebolaseq
|
public |
Tool for downloading and analyzing Ebola virus sequences
|
2025-03-07 |
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bioconductor-dada2
|
public |
Accurate, high-resolution sample inference from amplicon sequencing data
|
2025-03-07 |
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centrifuger
|
public |
Lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.
|
2025-03-07 |
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resistify
|
public |
A resistance gene annotation tool.
|
2025-03-07 |
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plannotate
|
public |
Webserver and command line tool for annotating engineered plasmids
|
2025-03-07 |
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viroconstrictor
|
public |
ViroConstrictor is a flexible pipeline for analysis of targeted viral sequencing data
|
2025-03-07 |
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snp2cell
|
public |
A package for finding enriched regulatory networks from GWAS and single cell data.
|
2025-03-07 |
|
savana
|
public |
SAVANA: a somatic structural variant caller for long-read data
|
2025-03-07 |
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bioconductor-glmgampoi
|
public |
Fit a Gamma-Poisson Generalized Linear Model
|
2025-03-06 |
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gmap-fusion
|
public |
GMAP-fusion is a utility for identifying candidate fusion transcripts based on transcript sequences reconstructed via RNA-Seq de novo transcriptome assembly.
|
2025-03-06 |
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transdecoder
|
public |
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
|
2025-03-06 |
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fusion-filter
|
public |
FusionFilter provides a common fusion-finding, filtering, and annotation framework for the Trinity Cancer Transcriptome Analysis Toolkit (CTAT).
|
2025-03-06 |
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fusion-inspector
|
public |
FusionInspector is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). FusionInspector assists in fusion transcript discovery by performing a supervised analysis of fusion predictions, attempting to recover and re-score evidence for such predictions. - https://github.com/FusionInspector/FusionInspector/wiki
|
2025-03-06 |
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flexynesis
|
public |
A deep-learning-based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.
|
2025-03-06 |
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psm-utils
|
public |
Common utilities for parsing and handling peptide-spectrum matches and search engine results.
|
2025-03-06 |
|
tower-cli
|
public |
The Tower CLI an interface to Nextflow Tower via the CLI
|
2025-03-06 |
|
gfastats
|
public |
The swiss army knife for genome assembly
|
2025-03-06 |
|
methbat
|
public |
A battery of methylation tools for PacBio HiFi reads
|
2025-03-06 |
|
tb-profiler
|
public |
Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from sequencing data
|
2025-03-06 |
|
enviroampdesigner
|
public |
Tool for training model and classifying reads from environmental ONT amplicon sequencing.
|
2025-03-06 |
|
autocycler
|
public |
A tool for generating consensus long-read assemblies for bacterial genomes.
|
2025-03-06 |
|
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.
|
2025-03-05 |
|
fast2q
|
public |
A Python3 program that counts sequence occurrences in FASTQ files.
|
2025-03-05 |
|
pigpen
|
public |
A package to quantify RNA localization using OINC-seq data
|
2025-03-05 |
|
hictk
|
public |
Blazing fast toolkit to work with .hic and .cool files
|
2025-03-05 |
|
ensembl-vep
|
public |
Ensembl Variant Effect Predictor
|
2025-03-05 |
