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mapdamage2
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public |
mapDamage: tracking and quantifying damage patterns in ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.
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2025-07-16 |
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automappa
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public |
Automappa: An interactive interface for exploration of metagenomes.
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2025-07-15 |
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famsa
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public |
Algorithm for large-scale multiple sequence alignments.
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2025-07-15 |
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codoff
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public |
codoff: program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the full genome.
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2025-07-15 |
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kleborate
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public |
Kleborate: a tool for typing and screening pathogen genome assemblies.
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2025-07-15 |
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hgvs
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public |
HGVS Parser, Formatter, Mapper, and Validator.
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2025-07-15 |
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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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2025-07-15 |
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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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2025-07-15 |
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seqnado
|
public |
Pipelines for genomics analysis
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2025-07-15 |
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amdirt
|
public |
amdirt: AncientMetagenomeDir Toolkit
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2025-07-15 |
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hgtools
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public |
Classes for Mercurial and Git repositories.
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2025-07-15 |
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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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2025-07-15 |
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hits
|
public |
Utilities for processing high-throughput sequencing experiments.
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2025-07-15 |
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gffcompare
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public |
GffCompare by Geo Pertea.
|
2025-07-15 |
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biocommons.seqrepo
|
public |
Python package for writing and reading a local collection of biological sequences.
|
2025-07-15 |
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ebolaseq
|
public |
Tool for downloading and analyzing Ebola virus sequences.
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2025-07-15 |
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aci
|
public |
Visualizes coverage for amplicons.
|
2025-07-15 |
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geofetch
|
public |
Downloads data and metadata from GEO and SRA and creates standard PEPs.
|
2025-07-15 |
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perl-inline
|
public |
Write Perl Subroutines in Other Programming Languages.
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2025-07-15 |
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synapseclient
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public |
Python client for Synapse.
|
2025-07-15 |
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bioconductor-alabaster.matrix
|
public |
Load and Save Artifacts from File
|
2025-07-15 |
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pathogen-profiler
|
public |
Library giving access to classes and functions to create a profiling tool to look for mutations from NGS data.
|
2025-07-15 |
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bioconductor-alabaster.base
|
public |
Save Bioconductor Objects To File
|
2025-07-15 |
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svync
|
public |
A tool to standardize VCF files from structural variant callers
|
2025-07-15 |
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r-rblast
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public |
Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.
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2025-07-15 |
