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lassaseq
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public |
Tool for downloading Lassa virus sequences
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2025-03-07 |
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snakemake-executor-plugin-kubernetes
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public |
A snakemake executor plugin for submission of jobs to Kubernetes
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2025-03-07 |
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ebolaseq
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public |
Tool for downloading and analyzing Ebola virus sequences
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2025-03-07 |
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bioconductor-dada2
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public |
Accurate, high-resolution sample inference from amplicon sequencing data
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2025-03-07 |
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centrifuger
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public |
Lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.
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2025-03-07 |
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resistify
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public |
A resistance gene annotation tool.
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2025-03-07 |
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plannotate
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public |
Webserver and command line tool for annotating engineered plasmids
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2025-03-07 |
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viroconstrictor
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public |
ViroConstrictor is a flexible pipeline for analysis of targeted viral sequencing data
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2025-03-07 |
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snp2cell
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public |
A package for finding enriched regulatory networks from GWAS and single cell data.
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2025-03-07 |
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savana
|
public |
SAVANA: a somatic structural variant caller for long-read data
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2025-03-07 |
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bioconductor-glmgampoi
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public |
Fit a Gamma-Poisson Generalized Linear Model
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2025-03-06 |
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gmap-fusion
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public |
GMAP-fusion is a utility for identifying candidate fusion transcripts based on transcript sequences reconstructed via RNA-Seq de novo transcriptome assembly.
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2025-03-06 |
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transdecoder
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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.
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2025-03-06 |
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fusion-filter
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public |
FusionFilter provides a common fusion-finding, filtering, and annotation framework for the Trinity Cancer Transcriptome Analysis Toolkit (CTAT).
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2025-03-06 |
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fusion-inspector
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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
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2025-03-06 |
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flexynesis
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public |
A deep-learning-based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.
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2025-03-06 |
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psm-utils
|
public |
Common utilities for parsing and handling peptide-spectrum matches and search engine results.
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2025-03-06 |
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tower-cli
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public |
The Tower CLI an interface to Nextflow Tower via the CLI
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2025-03-06 |
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gfastats
|
public |
The swiss army knife for genome assembly
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2025-03-06 |
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methbat
|
public |
A battery of methylation tools for PacBio HiFi reads
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2025-03-06 |
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tb-profiler
|
public |
Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from sequencing data
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2025-03-06 |
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enviroampdesigner
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public |
Tool for training model and classifying reads from environmental ONT amplicon sequencing.
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2025-03-06 |
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autocycler
|
public |
A tool for generating consensus long-read assemblies for bacterial genomes.
|
2025-03-06 |
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vuegen
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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.
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2025-03-05 |
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fast2q
|
public |
A Python3 program that counts sequence occurrences in FASTQ files.
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2025-03-05 |
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pigpen
|
public |
A package to quantify RNA localization using OINC-seq data
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2025-03-05 |
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hictk
|
public |
Blazing fast toolkit to work with .hic and .cool files
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2025-03-05 |
|
ensembl-vep
|
public |
Ensembl Variant Effect Predictor
|
2025-03-05 |
|
bwa-mem2
|
public |
The next version of bwa-mem
|
2025-03-05 |
|
rust-gtars
|
public |
Performance-critical tools to manipulate, analyze, and process genomic interval data.
|
2025-03-05 |
|
eastr
|
public |
Tool for emending alignments of spuriously spliced transcript reads.
|
2025-03-05 |
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snakemake-storage-plugin-sharepoint
|
public |
Snakemake storage plugin for reading and writing files on Microsoft SharePoint.
|
2025-03-05 |
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varlociraptor
|
public |
Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
|
2025-03-05 |
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kmercamel
|
public |
KmerCamel🐫 - compressing k-mer sets using masked superstrings
|
2025-03-05 |
|
seqnado
|
public |
Pipelines for genomics analysis
|
2025-03-05 |
|
r-tinyarray
|
public |
Gene Expression Omnibus(GEO) and The Cancer Genome Atlas(TCGA) are common bioinformatics public databases. We integrate the regular analysis and charts for expression data, to analyze and display the data concisely and intuitively.
|
2025-03-05 |
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orthanq
|
public |
Uncertainty aware HLA typing and general haplotype quantification.
|
2025-03-05 |
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ebi-eva-common-pyutils
|
public |
EBI EVA - Common Python Utilities
|
2025-03-05 |
|
argnorm
|
public |
Normalize antibiotic resistance genes (ARGs) abundance tables (e.g., from metagenomics) by using the ARO ontology (developed by CARD).
|
2025-03-05 |
|
bam-readcount
|
public |
bam-readcount generates metrics at single nucleotide positions.
|
2025-03-05 |
|
quantms-rescoring
|
public |
PSM rescoring python package with scripts and helpers for the quantms workflow
|
2025-03-05 |
|
simpleaf
|
public |
A rust framework to make using alevin-fry even simpler.
|
2025-03-05 |
|
reseek
|
public |
Protein structure alignment and search algorithm.
|
2025-03-05 |
|
sylph-tax
|
public |
Integrating taxonomic information into the sylph metagenome profiler.
|
2025-03-05 |
|
dnaapler
|
public |
Reorients assembled microbial sequences
|
2025-03-05 |
|
plink
|
public |
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
|
2025-03-04 |
|
nextflow
|
public |
A DSL for data-driven computational pipelines http://nextflow.io
|
2025-03-04 |
|
jbrowse2
|
public |
The JBrowse 2 Genome Browser
|
2025-03-04 |
|
pyopal
|
public |
Cython bindings and Python interface to Opal, a SIMD-accelerated pairwise aligner.
|
2025-03-04 |
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cayman
|
public |
A command-line profiling tool for profiling CAZyme abundances in metagenomic datasets.
|
2025-03-04 |
