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deepchopper-cli
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public |
A CLI for Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing.
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2025-03-25 |
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pyscenic
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public |
Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments.
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2025-03-25 |
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corneto
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public |
CORNETO: A Unified Framework for Omics-Driven Network Inference
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2025-03-25 |
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cell2cell
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public |
Inferring cell-cell interactions from transcriptomes with cell2cell
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2025-03-25 |
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coptr
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public |
Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.
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2025-03-25 |
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deepchopper
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public |
A Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing.
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2025-03-25 |
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libgff
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public |
A simple "libraryfication" of the GFF/GTF parsing code that is used in GFFRead codebase.
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2025-03-25 |
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mutyper
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public |
A Python package and command line utility for annotating the local ancestral sequence context of biallelic SNPs.
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2025-03-25 |
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flexiformatter
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public |
Moving flexiplex barcode and UMI to bam tags
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2025-03-25 |
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svision-pro
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public |
Neural-network-based long-read SV caller.
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2025-03-25 |
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ggcat
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public |
Compacted and colored de Bruijn graph construction and querying.
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2025-03-25 |
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steamboat
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public |
A collection of tools/scripts for microbial bioinformatics
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2025-03-25 |
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mikrokondo-tools
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public |
A collection of utilities to make using the mikrokondo pipeline easier
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2025-03-25 |
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pegas
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public |
PeGAS is a Snakemake pipeline for genome analysis
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2025-03-25 |
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pykofamsearch
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public |
Fast implementation of HMMSEARCH optimized for high-memory systems using PyHmmer.
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2025-03-25 |
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r-saccharis
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public |
A rendering package for creating phylogenetic trees from SACCHARIS .json and .tree files, in the R statistical computing language.
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2025-03-25 |
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zamp
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public |
zAMP: bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics
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2025-03-25 |
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genodsp
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public |
General workbench for processing signals along genomic (chromosomal) intervals
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2025-03-25 |
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telosearchlr
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public |
TeloSearchLR (telomere search using long sequencing reads) is a Python script for aiding the identificaiton of telomeric repeat motifs.
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2025-03-25 |
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snipe
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public |
SRA-Scale sequence QC and analysis
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2025-03-25 |
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pyhmmsearch
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public |
Fast implementation of HMMSEARCH optimized for high-memory systems using PyHmmer.
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2025-03-25 |
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splash
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public |
Unsupervised and reference-free unifying framework to discover regulated sequence variation through statistical analysis of k-mer composition in both DNA and RNA sequence.
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2025-03-25 |
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fastplong
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public |
Ultra-fast preprocessing and quality control for long-read sequencing data.
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2025-03-25 |
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gene-trajectory-python
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public |
Compute gene trajectories
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2025-03-25 |
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inmoose
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public |
InMoose is the Integrated Multi Omic Open Source Environment. It is a collection of tools for the analysis of omic data.
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2025-03-25 |
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cloudspades
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public |
A module of the SPAdes assembler aimed at genome assembly from linked read technologies (10x, Tellseq, Haplotagging).
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2025-03-25 |
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vclust
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public |
Fast and accurate tool for calculating ANI and clustering virus genomes and metagenomes.
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2025-03-25 |
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fmsi
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public |
FMSI - memory efficient k-mer set index based on masked superstrings and Burrows-Wheeler transform.
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2025-03-25 |
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r-chromvarmotifs
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public |
Stores several motifs as PWMatrixList objects for use in R with packages like motifmatchr and chromVAR.
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2025-03-25 |
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r-archr
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public |
This package is designed to streamline scATAC analyses in R.
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2025-03-25 |
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longcallr_nn
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public |
longcallR_nn is a variant caller specifically designed for long-read RNA-seq data utilizing a ResNet model.
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2025-03-25 |
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gafpack
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public |
Convert alignments to pangenome variation graphs to coverage maps
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2025-03-25 |
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seqspec
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public |
File format that describes data generated from genomics experiments. File format and seqspec tool enable uniform processing of genomics data.
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2025-03-25 |
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meta_eukaryome_detect
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public |
Pathogen, Parasite, Eukaryote and Virus detection in metagenomes.
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2025-03-25 |
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devider
|
public |
Haplotyping small sequences from heterogeneous long-read sequencing samples with a SNP-encoded positional de Bruijn graphs.
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2025-03-25 |
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cosigt
|
public |
Cosigt (COsine SImilarity-based GenoTyper)
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2025-03-25 |
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sfold
|
public |
Software for Statistical Folding of Nucleic Acids
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2025-03-25 |
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gfainject
|
public |
Inject alignment into pangenome graphs
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2025-03-25 |
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sipros
|
public |
Tools for stable isotopic mass spectrometry-based metaproteomics
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2025-03-25 |
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lz-ani
|
public |
Fast and accurate tool for calculating Average Nucleotide Identity (ANI) among virus and bacteria genomes
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2025-03-25 |
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patchify
|
public |
A library that helps you split image into small, overlappable patches, and merge patches back into the original image.
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2025-03-25 |
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tefinder
|
public |
Programs for transposable element search and annotation in large eukaryotic genome sequence.
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2025-03-25 |
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snk
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public |
A Snakemake CLI and Workflow Management System.
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2025-03-25 |
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snk-cli
|
public |
Dynamically generate CLIs from Snakemake configuration files
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2025-03-25 |
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mutamr
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public |
Stripped down tool for generation of annotated vcf from paired-end reads in a CPHL.
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2025-03-25 |
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mini3di
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public |
A NumPy port of the foldseek code for encoding protein structures to 3di.
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2025-03-25 |
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heliano
|
public |
HELIANO: A fast and accurate tool for detection of Helitron-like elements
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2025-03-25 |
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get_mnv
|
public |
Tool to identify Multi-Nucleotide Variants (MNVs) in genomic sequences.
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2025-03-25 |
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hmftools-peach
|
public |
Infer haplotypes for interpretation in a pharmacogenomic context
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2025-03-25 |
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pydustmasker
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public |
Python library for identification and masking of low-complexity regions in nucleotide sequences.
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2025-03-25 |
