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hanselx
|
public |
A graph-inspired data structure for determining likely chains of sequences from breadcrumbs of evidence
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2025-04-22 |
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desman
|
public |
De novo Extraction of Strains from MetAgeNomes
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2025-04-22 |
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perl-socket
|
public |
networking constants and support functions
|
2025-04-22 |
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r-stampp
|
public |
Allows users to calculate pairwise Nei's Genetic Distances (Nei 1972), pairwise Fixation Indexes (Fst) (Weir & Cockerham 1984) and also Genomic Relationship matrixes following Yang et al. (2010) in mixed and single ploidy populations. Bootstrapping across loci is implemented during Fst calculation to generate confidence intervals and p-values around pairwise Fst values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to handle missing data) and is coded to utilise multithreading where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects allowing integration with other packages such adegenet. Please refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, 13(5), 946-952. <doi
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2025-04-22 |
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r-pegas
|
public |
Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.
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2025-04-22 |
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r-qorts
|
public |
QoRTs toolkit for analysis, quality control, and data management of RNA-Seq
datasets.
|
2025-04-22 |
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bioconductor-snprelate
|
public |
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
|
2025-04-22 |
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bioconductor-gdsfmt
|
public |
R Interface to CoreArray Genomic Data Structure (GDS) Files
|
2025-04-22 |
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r-quorts
|
public |
The QoRTs software package is a fast, efficient, and portable multifunction toolkit designed to assist in the analysis, quality control, and data management of RNA-Seq datasets.
|
2025-04-22 |
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perl-extutils-constant
|
public |
generate XS code to import C header constants
|
2025-04-22 |
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fqtrim
|
public |
fqtrim is a versatile stand-alone utility that can be used to trim adapters, poly-A tails, terminal unknown bases (Ns) and low quality 3' regions in reads from high-throughput next-generation sequencing machines.
|
2025-04-22 |
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assemblerflow
|
public |
A Nextflow pipeline assembler for genomics. Pick your modules. Assemble them. Run the pipeline.
|
2025-04-22 |
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perl-extutils-cbuilder
|
public |
Compile and link C code for Perl modules
|
2025-04-22 |
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vqsr_cnn
|
public |
Variant quality score recalibration with Convolutional Neural Networks
|
2025-04-22 |
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mmvc
|
public |
Call variants based on a Bayesian multinomial mixture model.
|
2025-04-22 |
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pbhoover
|
public |
Variant caller for legacy and low coverage Pacific Biosciences' long-read sequencing data
|
2025-04-22 |
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brockman-pipeline
|
public |
Brockman Representation Of Chromatin by K-mers in Mark-Associated Nucleotides
|
2025-04-22 |
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amused
|
public |
Auditing Motifs Using Statistical Enrichment & Depletion
|
2025-04-22 |
|
ruby-dna-tools
|
public |
Various libraries containing useful functions for working with DNA sequences, written in ruby. Some tools are not specific to DNA.
|
2025-04-22 |
|
genometester4
|
public |
A toolkit for performing set operations - union, intersection and complement - on k-mer lists.
|
2025-04-22 |
|
segtools
|
public |
a python package for analyzing genomic segmentations
|
2025-04-22 |
|
comparative-annotation-toolkit
|
public |
A straightforward end-to-end pipeline that takes as input a HAL-format multiple whole genome alignment as well as a GFF3 file representing annotations on one high quality assembly in the HAL alignment, and produces a output GFF3 annotation on all target genomes chosen
|
2025-04-22 |
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ucsc-clustergenes
|
public |
Cluster genes from genePred tracks
|
2025-04-22 |
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amptk
|
public |
AMPtk: Amplicon tool kit for processing high throughput amplicon sequencing data.
|
2025-04-22 |
|
gblocks
|
public |
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
|
2025-04-22 |
