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earlgrey
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public |
Earl Grey: A fully automated TE curation and annotation pipeline
|
2025-04-02 |
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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.
|
2025-04-02 |
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ampligone
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public |
Ampligone is a tool which accurately removes primer sequences from FastQ NGS reads in an amplicon sequencing experiment
|
2025-04-01 |
|
bioconductor-data-packages
|
public |
A package to enable downloading and installation of Bioconductor data packages
|
2025-04-01 |
|
bioconductor-rnbeads.hg38
|
public |
RnBeads.hg38
|
2025-04-01 |
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r-shinyngs
|
public |
Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.
|
2025-04-01 |
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freyja
|
public |
Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.
|
2025-04-01 |
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profile_dists
|
public |
Profile Dists: Rapid calcualtion of allele profile distances and distance base querying
|
2025-03-31 |
|
lexicmap
|
public |
efficient sequence alignment against millions of prokaryotic genomes
|
2025-03-31 |
|
soi
|
public |
Orthology Index (OrthoIndex or OI) determines the orthology of a syntenic block.
|
2025-03-30 |
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ngsfetch
|
public |
Fast retrieval of metadata and fastq files with ffq and aria2c
|
2025-03-30 |
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blast
|
public |
BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.
|
2025-03-30 |
|
gempipe
|
public |
gempipe is a tool for the reconstruction of strain-specific genome-scale metabolic models.
|
2025-03-30 |
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r-corncob
|
public |
Statistical modeling for correlated count data using the beta-binomial distribution, described in Martin et al. (2020) <doi:10.1214/19-AOAS1283>. It allows for both mean and overdispersion covariates.
|
2025-03-30 |
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gsearch
|
public |
gsearch is an ultra-fast and scalable microbial genome search program based on MinHash-like metrics and graph-based approximate nearest neighbor search
|
2025-03-29 |
|
dbcan
|
public |
Standalone version of dbCAN annotation tool for automated CAZyme annotation.
|
2025-03-29 |
|
quantms-rescoring
|
public |
PSM rescoring python package with scripts and helpers for the quantms workflow
|
2025-03-29 |
|
aliceasm
|
public |
Efficient HiFi genome assembler producing haplotype-separated assemblies
|
2025-03-28 |
|
atlas
|
public |
ATLAS: Analysis Tools for Ancient and Low-depth Samples
|
2025-03-28 |
|
vambcore
|
public |
Performant backend functions for the Vamb binning tool
|
2025-03-28 |
|
nextclade
|
public |
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
|
2025-03-28 |
|
civicpy
|
public |
CIViC variant knowledgebase analysis toolkit.
|
2025-03-28 |
|
td2
|
public |
TD2: a tool to find protein coding regions in transcripts
|
2025-03-28 |
|
pytximport
|
public |
pytximport - gene count estimation from transcript-level quantification
|
2025-03-28 |
|
obonet
|
public |
Parse OBO formatted ontologies into networkx
|
2025-03-28 |
|
perl-namespace-autoclean
|
public |
Keep imports out of your namespace
|
2025-03-28 |
|
svtopovz
|
public |
Complex structural variant visualization for HiFi sequencing data: plotting tool.
|
2025-03-28 |
|
hmftools-linx
|
public |
LINX is an annotation, interpretation and visualisation tool for structural variants.
|
2025-03-28 |
|
taxmyphage
|
public |
Script to assign taxonomy to a bacteriophage at the genus and species level
|
2025-03-28 |
|
magneto
|
public |
MAGNETO is an automated snakemake workflow dedicated to MAG reconstruction from metagenomic data.
|
2025-03-28 |
|
genotypy
|
public |
Automatically detect genomic barcodes integrated into loci of interest from sequencing data
|
2025-03-28 |
|
seismic-rna
|
public |
SEISMIC-RNA software by the Rouskin Lab.
|
2025-03-28 |
|
nextstrain-cli
|
public |
The Nextstrain command-line interface (CLI)
|
2025-03-28 |
|
sequenoscope
|
public |
sequenoscope is a versatile bioinformatic pipeline for the analysis of sequencing data.
|
2025-03-28 |
|
psauron
|
public |
PSAURON: a machine learning model for rapid assessment of protein coding gene annotation
|
2025-03-28 |
|
perl-math-bigint
|
public |
Arbitrary size floating point math package
|
2025-03-28 |
|
genmod
|
public |
Annotate genetic inheritance models in variant files
|
2025-03-28 |
|
nextflow
|
public |
A DSL for data-driven computational pipelines http://nextflow.io
|
2025-03-28 |
|
yleaf
|
public |
Yleaf - A tool for Y-chromosome haplogroup prediction
|
2025-03-28 |
|
vcflib
|
public |
Command-line tools for manipulating VCF files.
|
2025-03-28 |
|
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>.
|
2025-03-28 |
|
slivar
|
public |
filter/annotate variants in VCF/BCF format with simple expressions
|
2025-03-28 |
|
commec
|
public |
commec: a free, open-source, globally available tool for DNA sequence screening
|
2025-03-28 |
|
pisad
|
public |
pisad - Phsaed Intraspecies Sample Anomalies Detection tool
|
2025-03-28 |
|
planemo
|
public |
Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).
|
2025-03-28 |
|
ena-webin-cli
|
public |
Data submissions to ENA can be made using the Webin command line submission interface (Webin-CLI).
|
2025-03-28 |
|
rpsbproc
|
public |
RpsbProc, the post-RPSBLAST Processing Utility.
|
2025-03-28 |
|
pegasuspy
|
public |
An efficient Python analysis tool which scales to transcriptomes of millions of single cells.
|
2025-03-28 |
|
amiga
|
public |
Analysis of Microbial Growth Assays
|
2025-03-28 |
|
iow
|
public |
Implementation of Balanced Parentheses
|
2025-03-28 |
