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iow
|
public |
Implementation of Balanced Parentheses
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2025-03-28 |
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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 |
|
mgnify-pipelines-toolkit
|
public |
Collection of scripts and tools for MGnify pipelines.
|
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 |
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lovis4u
|
public |
Loci Visualisation Tool.
|
2025-03-28 |
|
olivar
|
public |
Olivar PCR tiling design
|
2025-03-28 |
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pybwa
|
public |
Pybwa is a python module that makes it easy to align sequence data. It is a lightweight wrapper of bwa.
|
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 |
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nbitk
|
public |
nbitk: Naturalis BioInformatics ToolKit
|
2025-03-27 |
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arvados-python-client
|
public |
Python API for Arvados
|
2025-03-27 |
|
bam2plot
|
public |
Plot of coverage from bam file
|
2025-03-27 |
|
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.
|
2025-03-27 |
|
relecov-tools
|
public |
Tools for managing and processing of relecov data.
|
2025-03-27 |
|
perl-graph
|
public |
a Perl extension for keeping data partially sorted
|
2025-03-27 |
|
oarfish
|
public |
oarfish is a tool for fast, accurate and versatile transcript quantification from long-read RNA-seq data
|
2025-03-27 |
|
bioconda-utils
|
public |
Utilities for building and managing bioconda recipes.
|
2025-03-27 |
|
hiphase
|
public |
Small and structural variant phasing tool for PacBio HiFi reads
|
2025-03-27 |
|
zdb
|
public |
zDB is both a bacterial comparative genomics pipeline and a tool to visualize the results
|
2025-03-27 |
|
snakemake-interface-executor-plugins
|
public |
This package provides a stable interface for interactions between Snakemake and its executor plugins.
|
2025-03-27 |
|
snakemake-storage-plugin-fs
|
public |
A Snakemake storage plugin that reads and writes from a locally mounted filesystem using rsync.
|
2025-03-27 |
|
latch
|
public |
The Latch python bioinformatics framework
|
2025-03-27 |
|
arriba
|
public |
Fast and accurate gene fusion detection from RNA-Seq data
|
2025-03-26 |
|
sistr_cmd
|
public |
Salmonella In Silico Typing Resource (SISTR) commandline tool for serovar prediction
|
2025-03-26 |
|
lexicmap
|
public |
efficient sequence alignment against millions of prokaryotic genomes
|
2025-03-26 |
|
snippy
|
public |
Rapid bacterial SNP calling and core genome alignments
|
2025-03-26 |
|
shiba2sashimi
|
public |
A utility for creating sashimi plot from Shiba output
|
2025-03-26 |
|
earlgrey
|
public |
Earl Grey: A fully automated TE curation and annotation pipeline
|
2025-03-26 |
|
graphembed
|
public |
Efficient and Robust Graph/Network Embedding via High-Order Proximity Preservation or Recursive Sketching.
|
2025-03-26 |
|
grz-pydantic-models
|
public |
Pydantic models for the GRZ metadata schema
|
2025-03-25 |
|
fastcov
|
public |
This package installs fastcov and all it's dependencies. fastcov is used to plot coverage plots based on BAM files.
|
2025-03-25 |
|
alientrimmer
|
public |
Tool for trimming non-confident bases and alien oligo-nucleotide sequences from sequencing reads.
|
2025-03-25 |
|
bcftools-liftover-plugin
|
public |
Tools to work with GWAS-VCF summary statistics files (liftover plugin only)
|
2025-03-25 |
|
longcalld
|
public |
longcallD: local-haplotagging-based small and structural variant calling
|
2025-03-25 |
|
isotools
|
public |
Framework for the analysis of long read transcriptome sequencing data
|
2025-03-25 |
|
spacedust
|
public |
De novo discovery of conserved gene clusters in microbial genomes with Spacedust
|
2025-03-25 |
|
fastga
|
public |
FastGA - A Fast Genome Aligner.
|
2025-03-25 |
|
snakemake-interface-logger-plugins
|
public |
This package provides a stable interface for interactions between Snakemake and its logger plugins.
|
2025-03-25 |
|
mysterymaster
|
public |
Graphical Oxford Nanopore read demultiplexer
|
2025-03-25 |
|
gencube
|
public |
GenCube enables researchers to search for, download, retrieve metadata, and unify genome assemblies and diverse types of annotations for sequencing-based experimental data.
|
2025-03-25 |
|
vcf_parser
|
public |
Small library for parsing vcf files.
|
2025-03-25 |
|
deacon
|
public |
Fast alignment-free sequence filter
|
2025-03-25 |
|
snakemake-executor-plugin-aws-batch
|
public |
A Snakemake executor plugin for submitting jobs to AWS Batch.
|
2025-03-25 |
|
cctyper
|
public |
CRISPRCasTyper: Automatic detection and subtyping of CRISPR-Cas operons
|
2025-03-25 |
|
snakemake-storage-plugin-xrootd
|
public |
A Snakemake storage plugin for XRootD storage
|
2025-03-25 |
|
mutserve
|
public |
Mutserve2 is a variant caller for the mitochondrial genome to detect homoplasmic and heteroplasmic sites in sequence data.
|
2025-03-25 |
|
hippunfold-dev
|
public |
Meta-package that installs hippunfold with development dependencies.
|
2025-03-25 |
