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clever-toolkit
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public |
The clever toolkit (CTK) is a suite of tools to analyze next-generation sequencing data and, in particular, to discover and genotype insertions and deletions from paired-end reads.
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2024-06-18 |
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nanomath
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public |
A few simple math function for other Oxford Nanopore processing scripts
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2024-06-14 |
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pbcopper
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public |
Core C++ library for data structures, algorithms, and utilities
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2024-06-14 |
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dinopy
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public |
DNA input and output library for Python and Cython. Includes reader and writer for FASTA and FASTQ files, support for samtools faidx files, and generators for solid and gapped q-grams (k-mers).
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2024-06-13 |
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jcvi
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public |
Python utility libraries on genome assembly, annotation, and comparative genomics
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2024-06-13 |
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genomelake
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public |
Simple and efficient random access to genomic data for deep learning models.
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2024-06-12 |
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genometools-genometools
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public |
GenomeTools genome analysis system.
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2024-06-12 |
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sortmerna
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public |
SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads.
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2024-06-12 |
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perl-getopt-long
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public |
Module to handle parsing command line options
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2024-06-12 |
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peakachu
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public |
Peak calling tool for CLIP-seq data.
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2024-06-11 |
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elprep
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public |
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.
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2024-06-11 |
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gembs
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public |
gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).
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2024-06-09 |
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dsh-bio
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public |
Tools for BED, FASTA, FASTQ, GAF, GFA1/2, GFF3, PAF, SAM, and VCF files
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2024-06-09 |
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frogs
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public |
FROGS is a workflow designed to metabarcoding sequence analysis
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2024-06-07 |
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perl-dbm-deep
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public |
A pure perl multi-level hash/array DBM that supports transactions
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2024-06-07 |
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squid
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public |
Detector for fusion-gene and non-fusion-gene transcriptomic structural variations from RNA-seq data
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2024-06-06 |
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sonlib
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public |
Small general purpose library for C and Python with focus on bioinformatics.
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2024-06-06 |
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ariba
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public |
ARIBA: Antibiotic Resistance Identification By Assembly
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2024-06-05 |
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igblast
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public |
A tool for analyzing immunoglobulin (IG) and T cell receptor (TR) sequences
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2024-06-05 |
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perl-test2-suite
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public |
Distribution with a rich set of tools built upon the Test2 framework.
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2024-06-05 |
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forgi
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public |
RNA Graph Library
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2024-06-05 |
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ragout
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public |
Chromosome-level scaffolding using multiple references
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2024-06-05 |
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peakranger
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public |
PeakRanger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data.
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2024-06-05 |
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commet
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public |
Comparing and combining multiple metagenomic datasets
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2024-06-05 |
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mztosqlite
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public |
Convert proteomics data files into a SQLite database.
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2024-06-05 |
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squeakr
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public |
An Exact and Approximate k-mer Counting System
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2024-06-04 |
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dawg
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public |
DNA Assembly with Gaps (Dawg) is an application designed to simulate the evolution of recombinant DNA sequences in continuous time based on the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation.
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2024-06-04 |
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cassiopee
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public |
scan an input genomic sequence (dna/rna/protein) and search for a subsequence with exact match or allowing substitutions (Hamming distance) and/or insertion/deletions
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2024-06-04 |
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mob_suite
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public |
MOB-suite is a set of tools for finding, typing and reconstruction of plasmids from draft and complete genome assemblies.
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2024-06-04 |
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airr
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public |
AIRR Community Data Representation Standard reference library for antibody and TCR sequencing data. Citations: AIRR standards <doi:10.5281/zenodo.1185414>.
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2024-06-03 |
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dendropy
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public |
A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.
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2024-06-02 |
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vcf2maf
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public |
Convert a VCF into a MAF where each variant is annotated to only one of all possible gene isoforms.
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2024-05-31 |
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perl-spreadsheet-parseexcel
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public |
Read information from an Excel file.
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2024-05-31 |
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bioconductor-contibait
|
public |
Improves Early Build Genome Assemblies using Strand-Seq Data
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2024-05-30 |
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msstitch
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public |
MS proteomics post processing utilities
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2024-05-28 |
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bioconductor-exomecopy
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public |
Copy number variant detection from exome sequencing read depth
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2024-05-28 |
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perl-math-bigint
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public |
Arbitrary size floating point math package
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2024-05-28 |
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smallgenomeutilities
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public |
A collection of scripts that are useful for dealing with viral RNA NGS data.
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2024-05-27 |
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toil
|
public |
A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python
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2024-05-24 |
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snpeff
|
public |
Genetic variant annotation and effect prediction toolbox
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2024-05-23 |
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krakenuniq
|
public |
Metagenomics classifier with unique k-mer counting for more specific results
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2024-05-23 |
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pymzml
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public |
high-throughput mzML parsing
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2024-05-10 |
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bioconductor-maigespack
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public |
Functions to handle cDNA microarray data, including several methods of data analysis
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2024-05-10 |
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yaggo
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public |
Yaggo is a tool to generate command line parsers for C++. Yaggo stands for "Yet Another GenGetOpt" and is inspired by GNU Gengetopt.
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2024-05-09 |
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bioconductor-cohcap
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public |
CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data
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2024-05-09 |
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r-workflowscriptscommon
|
public |
Common functions for making R function wapper scripts. Functions in R packages are hard to call when building workflows outside of R, so this package is used by other packages (e.g. r-seurat-scripts) to add sets of simple wrappers with robust argument parsing.
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2024-05-07 |
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mockinbird
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public |
A fully automatic and reproducible PAR-CLIP analysis pipeline
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2024-05-07 |
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pygenometracks
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public |
Standalone program and library to plot beautiful genome browser tracks.
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2024-05-07 |
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seqlogo
|
public |
Python port of the R Bioconductor `seqlogo` package
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2024-05-03 |
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ddocent
|
public |
dDocent is an interactive bash wrapper to QC, assemble, map, and call SNPs from all types of RAD data
|
2024-05-03 |
