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hyphy
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public |
An open-source software package for comparative sequence analysis using stochastic evolutionary models.
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2025-09-24 |
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igv-reports
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public |
Creates self-contained html pages for visual variant review with IGV (igv.js).
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2025-09-24 |
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dbgraph
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public |
A graph-centric approach for metagenome-guided peptide identification in metaproteomics.
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2025-09-24 |
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miranda
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public |
An algorithm for finding genomic targets for microRNAs
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2025-09-24 |
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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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2025-09-24 |
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ariba
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public |
ARIBA: Antibiotic Resistance Identification By Assembly.
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2025-09-23 |
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ra
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public |
Ra is short for RNA Assembler and it is a C++ implementation of an overlap-layout-consensus transcriptome assembler.
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2025-09-23 |
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vmatch
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public |
The Vmatch large scale sequence analysis software.
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2025-09-23 |
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links
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public |
Long Interval Nucleotide K-mer Scaffolder
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2025-09-23 |
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pywfa
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public |
A python wrapper for wavefront alignment using WFA2-lib
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2025-09-23 |
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longtr
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public |
Tandem repeat genotyping with long reads.
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2025-09-23 |
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metilene
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public |
Fast and sensitive detection of differential DNA methylation
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2025-09-23 |
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carp
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public |
carp - quantify the rearrangement complexity of pangenomes and their graphs.
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2025-09-23 |
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ncbitax2lin
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public |
NCBItax2lin
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2025-09-23 |
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humanfilt
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public |
WGS human-read filtering with auto-downloaded human references
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2025-09-23 |
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bin2cell
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public |
Join subcellular Visium HD bins into cells
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2025-09-23 |
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gather
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public |
Assembly of heavy and light chain BCRs using De Bruijn graphs.
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2025-09-23 |
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novoloci
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public |
Haplotype-aware assembler for complex regions and small genomes (ONT/HiFi).
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2025-09-23 |
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switchtfi
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public |
Implementation of the SwitchTFI method as presented in: https://doi.org/10.1101/2025.01.20.633856
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2025-09-23 |
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cagecleaner
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public |
Genomic redundancy removal tool for cblaster hit sets.
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2025-09-23 |
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ipcr
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public |
In-silico PCR with mismatch thresholds and pretty alignment output.
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2025-09-23 |
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gap2seq
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public |
Gap2Seq is a tool for filling gaps between contigs in genome assemblies.
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2025-09-23 |
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ltr_finder
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public |
LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.
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2025-09-23 |
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sga
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public |
SGA - String Graph Assembler. SGA is a de novo assembler for DNA sequence reads. It is based on Gene Myers string graph formulation of assembly and uses the FM-index/Burrows-Wheeler transform to efficiently find overlaps between sequence reads.
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2025-09-23 |
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altex-be
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public |
Automatically design sgRNA for exon skipping with many base editors.
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2025-09-23 |
