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forgi
|
public |
RNA Graph Library
|
2025-04-22 |
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dig2
|
public |
dig2 is a simple but flexible in silico digester of protein sequences in the FASTA format. It allows for almost any enzyme to be simulated, including MS/MS enzymes to generate CID or ECD/ETD fragments.
|
2025-04-22 |
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gretel
|
public |
An algorithm for recovering haplotypes from metagenomes
|
2025-04-22 |
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bibliospec
|
public |
The BiblioSpec Spetral Library tool suite
|
2025-04-22 |
|
itero
|
public |
A pipeline for iterative, guided contig assembly that integrates spades, bwa, and samtools to produce assembled contigs.
|
2025-04-22 |
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rnaclust
|
public |
A tool for clustering of RNAs based on their secondary structures using LocARNA
|
2025-04-22 |
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biopet-vcfstats
|
public |
Vcfstats is a tool that can generate metrics from a vcf file.
|
2025-04-22 |
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bioconductor-interest
|
public |
Intron-Exon Retention Estimator
|
2025-04-22 |
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akt
|
public |
Ancestry and Kinship Tools (AKT)
|
2025-04-22 |
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staramr
|
public |
Scan genome contigs against the ResFinder and PointFinder databases
|
2025-04-22 |
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mustang
|
public |
Mustang is a program that implements an algorithm for structural alignment of multiple protein structures.
|
2025-04-22 |
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perl-perl4-corelibs
|
public |
libraries historically supplied with Perl 4
|
2025-04-22 |
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ac-diamond
|
public |
AC-DIAMOND is a DNA-protein alignment tool
|
2025-04-22 |
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hanselx
|
public |
A graph-inspired data structure for determining likely chains of sequences from breadcrumbs of evidence
|
2025-04-22 |
|
desman
|
public |
De novo Extraction of Strains from MetAgeNomes
|
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
|
2025-04-22 |
|
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.
|
2025-04-22 |
|
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 |
|
bioconductor-gdsfmt
|
public |
R Interface to CoreArray Genomic Data Structure (GDS) Files
|
2025-04-22 |
|
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 |
|
perl-extutils-constant
|
public |
generate XS code to import C header constants
|
2025-04-22 |
|
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 |
|
assemblerflow
|
public |
A Nextflow pipeline assembler for genomics. Pick your modules. Assemble them. Run the pipeline.
|
2025-04-22 |
