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ruby-dna-tools
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public |
Various libraries containing useful functions for working with DNA sequences, written in ruby. Some tools are not specific to DNA.
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2023-06-16 |
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pbhoover
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public |
Variant caller for legacy and low coverage Pacific Biosciences' long-read sequencing data
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2023-06-16 |
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perl-extutils-constant
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public |
generate XS code to import C header constants
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2023-06-16 |
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perl-perl4-corelibs
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public |
libraries historically supplied with Perl 4
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2023-06-16 |
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ac-diamond
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public |
AC-DIAMOND is a DNA-protein alignment tool
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2023-06-16 |
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r-stampp
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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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2023-06-16 |
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rnaclust
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public |
A tool for clustering of RNAs based on their secondary structures using LocARNA
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2023-06-16 |
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vqsr_cnn
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public |
Variant quality score recalibration with Convolutional Neural Networks
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2023-06-16 |
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hanselx
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public |
A graph-inspired data structure for determining likely chains of sequences from breadcrumbs of evidence
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2023-06-16 |
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brockman-pipeline
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public |
Brockman Representation Of Chromatin by K-mers in Mark-Associated Nucleotides
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2023-06-16 |
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amused
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public |
Auditing Motifs Using Statistical Enrichment & Depletion
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2023-06-16 |
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gretel
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public |
An algorithm for recovering haplotypes from metagenomes
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2023-06-16 |
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comparative-annotation-toolkit
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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
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2023-06-16 |
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segtools
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public |
a python package for analyzing genomic segmentations
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2023-06-16 |
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assemblerflow
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public |
A Nextflow pipeline assembler for genomics. Pick your modules. Assemble them. Run the pipeline.
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2023-06-16 |
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satsuma2
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public |
FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing
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2023-06-16 |
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gblocks
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public |
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
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2023-06-16 |
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fusion-filter
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public |
FusionFilter provides a common fusion-finding, filtering, and annotation framework for the Trinity Cancer Transcriptome Analysis Toolkit (CTAT).
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2023-06-16 |
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perl-perl-ostype
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public |
Map Perl operating system names to generic types
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2023-06-16 |
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fseq
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public |
F-Seq: A feature density estimator for high-throughput sequence tags
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2023-06-16 |
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libdeflate
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public |
libdeflate is a library for fast, whole-buffer DEFLATE-based compression and decompression.
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2023-06-16 |
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perl-file-tee
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public |
replicate data sent to a Perl stream
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2023-06-16 |
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perl-bio-mlst-check
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public |
Multilocus sequence type checking using blast
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2023-06-16 |
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perl-super
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public |
control superclass method dispatch
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2023-06-16 |
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sloika
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public |
Sloika is Oxford Nanopore Technologies' software for training neural network models for base calling
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2023-06-16 |
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perl-file-touch
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public |
update file access and modification times, optionally creating files if needed
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2023-06-16 |
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perl-test-mockmodule
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public |
Override subroutines in a module for unit testing
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2023-06-16 |
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smoove
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public |
structural variant calling and genotyping with existing tools, but, smoothly
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2023-06-16 |
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mamotif
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public |
An integrative toolkit for detecting cell type-specific regulators
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2023-06-16 |
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libssw
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public |
An SIMD Smith-Waterman C/C++/Python/Java Library for Use in Genomic Applications
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2023-06-16 |
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drax
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public |
A pipeline for Detecting Resistome Associated taXa.
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2023-06-16 |
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chromosomer
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public |
A reference-assisted assembly tool for producing draft chromosome sequences.
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2023-06-16 |
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protk
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public |
protk (Proteomics toolkit)
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2023-06-16 |
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mikado
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public |
A Python3 annotation program to select the best gene model in each locus
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2023-06-16 |
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bioformats
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public |
A collection of Python classes to handle bioinformatics data.
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2023-06-16 |
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suppa
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public |
A tool to study splicing across multiple conditions at high speed and accuracy.
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2023-06-16 |
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tpp
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public |
The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics developed at the Seattle Proteome Center. The Bioconda package includes the command-line versions of the TPP toolset. These programs include tools for validation (PeptideProphet, iProphet, ProteinProphet, Mayu) and quantification (XPRESS, ASAPRatio, Libra) as well as a number of parsers and converters (Out2XML, Mascot2XML, Tandem2XML, etc).
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2023-06-16 |
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perl-findbin-libs
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public |
locate and a 'use lib' or export directories based on $FindBin::Bin.
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2023-06-16 |
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perl-module-fromperlver
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public |
install modules compatible with the running perl.
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2023-06-16 |
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k-slam
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public |
k-SLAM is a program for alignment based metagenomic analysis of large sets of high-throughput sequence data.
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2023-06-16 |
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adapterremovalfixprefix
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public |
Fixes adapter removal prefixes to make sure no clashing read names are in the output.
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2023-06-16 |
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circularmapper
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public |
A method to improve mappings on circular genomes, using the BWA mapper.
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2023-06-16 |
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cistrome_beta
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public |
Binding and Expression Target Analysis of ChIP-seq TF with differential gene expression
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2023-06-16 |
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marge
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public |
Model-based Analysis of Regulation of Gene Expression
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2023-06-16 |
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vcf2genome
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public |
A tool to create a draft genome file out of a GATK VCF file and enabling users to filter the VCF in a single step.
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2023-06-16 |
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pispino
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public |
PISPINO (PIpits SPIN-Off tools): Bioinformatics toolkits for processing NGS data
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2023-06-16 |
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metagene_annotator
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public |
MetaGeneAnnotator is a gene-finding program for prokaryote and phage
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2023-06-16 |
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pydnase
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public |
DNase-seq analysis library
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2023-06-16 |
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snakeparse
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public |
Making Snakemake workflows into full-fledged command line tools since 1999.
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2023-06-16 |
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krakenhll
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public |
KrakenHLL metagenomics classification method with unique k-mer counting for more specific results
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2023-06-16 |
