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cstag-cli
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public |
Command line interface of cstag to manipulate the minimap2's CS tag
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2025-04-22 |
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rbpbench
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public |
Evaluate CLIP-seq and other genomic region data using a comprehensive collection of known RBP binding motifs
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2025-04-22 |
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sylph
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public |
sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.
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2025-04-22 |
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ms-entropy
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public |
This package provides a Python implementation of calculating spectral entropy, entropy similarity, and Flash entropy search for mass spectrometry data.
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2025-04-22 |
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happy-python
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public |
Haploidy and Size Completeness Estimation with Python
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2025-04-22 |
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dnamarkmaker
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public |
DNAMarkMaker: pipeline to development ARMS and CAPS marker
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2025-04-22 |
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dajin2
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public |
One-step genotyping tools for targeted long-read sequencing
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2025-04-22 |
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binette
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public |
A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.
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2025-04-22 |
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kinship-read
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public |
Relationship Estimation from Ancient DNA version 2 (READv2)
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2025-04-22 |
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riblast
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public |
RIblast is ultrafast RNA-RNA interaction prediction software.
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2025-04-22 |
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crispector2
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public |
Accurate estimation of off-target editing activity from comparative NGS data
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2025-04-22 |
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checkatlas
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public |
One liner tool to check the quality of your single-cell atlases.
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2025-04-22 |
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binny
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public |
An automated binning algorithm to recover high-quality genomes from complex metagenomic datasets. Note: This is a development version.
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2025-04-22 |
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r-pathfindr
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public |
Enrichment analysis enables researchers to uncover mechanisms underlying a phenotype. However, conventional methods for enrichment analysis do not take into account protein-protein interaction information, resulting in incomplete conclusions. pathfindR is a tool for enrichment analysis utilizing active subnetworks. The main function identifies active subnetworks in a protein-protein interaction network using a user-provided list of genes and associated p values. It then performs enrichment analyses on the identified subnetworks, identifying enriched terms (i.e. pathways or, more broadly, gene sets) that possibly underlie the phenotype of interest. pathfindR also offers functionalities to cluster the enriched terms and identify representative terms in each cluster, to score the enriched terms per sample and to visualize analysis results. The enrichment, clustering and other methods implemented in pathfindR are described in detail in Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Front. Genet. <doi:10.3389/fgene.2019.00858>.
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2025-04-22 |
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tadrep
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public |
TaDRep: Targeted Detection and Reconstruction of Plasmids
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2025-04-22 |
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kmd_hmdb_api_client
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public |
The KMD HMDB project API Client
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2025-04-22 |
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umi-transfer
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public |
A tool for transferring Unique Molecular Identifiers (UMIs) from a separate FastQ file.
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2025-04-22 |
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ipapy2
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public |
Integrated Probabilistic Annotation (IPA) 2.0 - Python implementation
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2025-04-22 |
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physiofit
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public |
Calculate extracellular fluxes from metabolite concentrations and biomass data
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2025-04-22 |
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hictkpy
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public |
Python bindings for hictk: read and write .cool and .hic files directly from Python
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2025-04-22 |
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xengsort
|
public |
A fast xenograft read sorter based on space-efficient k-mer hashing
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2025-04-22 |
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sativa
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public |
SATIVA Semi-Automatic Taxonomy Improvement and Validation Algorithm
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2025-04-22 |
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arcsv
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public |
A pipeline to detect SV in archaic human
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2025-04-22 |
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sdeper
|
public |
Spatial Deconvolution method with Platform Effect Removal
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2025-04-22 |
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r-eggnog
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public |
EggNOG database annotations.
|
2025-04-22 |
