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frogs
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public |
FROGS is a workflow designed to metabarcoding sequence analysis
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2025-04-02 |
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stare-abc
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public |
Calculate Gene-TF affinities via enhancer-gene interactions
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2025-04-02 |
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eva-sub-cli
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public |
EVA Submission Command Line Interface
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2025-04-02 |
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earlgrey
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public |
Earl Grey: A fully automated TE curation and annotation pipeline
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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
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2025-04-01 |
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bioconductor-data-packages
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public |
A package to enable downloading and installation of Bioconductor data packages
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2025-04-01 |
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bioconductor-rnbeads.hg38
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public |
RnBeads.hg38
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2025-04-01 |
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r-shinyngs
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public |
Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.
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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
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2025-03-31 |
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soi
|
public |
Orthology Index (OrthoIndex or OI) determines the orthology of a syntenic block.
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2025-03-30 |
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ngsfetch
|
public |
Fast retrieval of metadata and fastq files with ffq and aria2c
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2025-03-30 |
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blast
|
public |
BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.
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2025-03-30 |
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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
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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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civicpy
|
public |
CIViC variant knowledgebase analysis toolkit.
|
2025-03-28 |
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td2
|
public |
TD2: a tool to find protein coding regions in transcripts
|
2025-03-28 |
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pytximport
|
public |
pytximport - gene count estimation from transcript-level quantification
|
2025-03-28 |
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obonet
|
public |
Parse OBO formatted ontologies into networkx
|
2025-03-28 |
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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 |
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hmftools-linx
|
public |
LINX is an annotation, interpretation and visualisation tool for structural variants.
|
2025-03-28 |
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taxmyphage
|
public |
Script to assign taxonomy to a bacteriophage at the genus and species level
|
2025-03-28 |
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magneto
|
public |
MAGNETO is an automated snakemake workflow dedicated to MAG reconstruction from metagenomic data.
|
2025-03-28 |
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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 |
|
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 |
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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>.
|
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 |
|
sc-musketeers
|
public |
A tri-partite modular autoencoder for addressing imbalanced cell type annotation and batch effect reduction
|
2025-03-28 |
|
mi-pimento
|
public |
A PrIMEr infereNce TOolkit to facilitate large-scale calling of metabarcoding amplicon sequence variants
|
2025-03-28 |
|
seq2squiggle
|
public |
End-to-end simulation of nanopore sequencing signals with feed-forward transformers
|
2025-03-28 |
|
novae
|
public |
Graph-based foundation model for spatial transcriptomics data
|
2025-03-28 |
|
lovis4u
|
public |
Loci Visualisation Tool.
|
2025-03-28 |
|
olivar
|
public |
Olivar PCR tiling design
|
2025-03-28 |
|
spacerextractor
|
public |
Extract CRISPR spacers from metagenome short reads.
|
2025-03-28 |
|
mlstdb
|
public |
A Python package to update and manage the MLST database for the MLST tool.
|
2025-03-27 |
|
starcatpy
|
public |
Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with predefined gene expression programs.
|
2025-03-27 |
