med-bio-dev

dep: [med-config] (= 3.9.0)

Debian Med general config package

dep: [med-tasks] (= 3.9.0)

Debian Med tasks for tasksel

rec: [bio-tradis]

analyse the output from TraDIS analyses of genomic sequences

rec: [biobambam2]

tools for early stage alignment file processing

rec: [bioperl]

Perl tools for computational molecular biology

rec: [bioperl-run]

BioPerl wrappers: scripts

rec: [biosquid]

utilities for biological sequence analysis

rec: [cwltool]

Common Workflow Language reference implementation

rec: [gffread]

GFF/GTF format conversions, region filtering, FASTA sequence extraction

rec: [goby-java]

next-generation sequencing data and results analysis tool

rec: [libace-perl]

Object-Oriented Access to ACEDB Databases

rec: [libai-fann-perl]

Perl wrapper for the FANN library

rec: [libbambamc-dev]

Development files for reading and writing BAM (genome alignment) files

rec: [libbamtools-dev]

C++ API for manipulating BAM (genome alignment) files

rec: [libbigwig-dev]

C library for handling bigWig files - header files

rec: [libbio-alignio-stockholm-perl]

stockholm sequence input/output stream

rec: [libbio-asn1-entrezgene-perl]

parser for NCBI Entrez Gene and NCBI Sequence records

rec: [libbio-chado-schema-perl]

DBIx::Class layer for the Chado database schema

rec: [libbio-cluster-perl]

BioPerl cluster modules

rec: [libbio-coordinate-perl]

BioPerl modules for working with biological coordinates

rec: [libbio-das-lite-perl]

implementation of the BioDas protocol

rec: [libbio-db-biofetch-perl]

Database object interface to BioFetch retrieval

rec: [libbio-db-embl-perl]

Database object interface for EMBL entry retrieval

rec: [libbio-db-hts-perl]

Perl interface to the HTS library

rec: [libbio-db-ncbihelper-perl]

collection of routines useful for queries to NCBI databases

rec: [libbio-db-seqfeature-perl]

Normalized feature for use with Bio::DB::SeqFeature::Store

rec: [libbio-eutilities-perl]

BioPerl interface to the Entrez Programming Utilities (E-utilities)

rec: [libbio-featureio-perl]

Modules for reading, writing, and manipulating sequence features

rec: [libbio-graphics-perl]

Generate GD images of Bio::Seq objects

rec: [libbio-mage-perl]

Container module for classes in the MAGE package: MAGE

rec: [libbio-mage-utils-perl]

Extra modules for classes in the MAGE package: MAGE

rec: [libbio-primerdesigner-perl]

Perl module to design PCR primers using primer3 and epcr

rec: [libbio-samtools-perl]

Perl interface to SamTools library for DNA sequencing

rec: [libbio-scf-perl]

Perl extension for reading and writing SCF sequence files

rec: [libbio-tools-phylo-paml-perl]

Bioperl interface to the PAML suite

rec: [libbio-tools-run-alignment-clustalw-perl]

Bioperl interface to Clustal W

rec: [libbio-tools-run-alignment-tcoffee-perl]

Bioperl interface to T-Coffee

rec: [libbio-tools-run-remoteblast-perl]

Object for remote execution of the NCBI Blast via HTTP

rec: [libbio-variation-perl]

BioPerl variation-related functionality

rec: [libbiojava-java]

Java API to biological data and applications (default version)

rec: [libbiojava6-java]

Java API to biological data and applications (version 6)

rec: [libbioparser-dev]

library for parsing several formats in bioinformatics

rec: [libblasr-dev]

tools for aligning PacBio reads to target sequences (development files)

rec: [libbpp-core-dev]

Bio++ Core library development files

rec: [libbpp-phyl-dev]

Bio++ Phylogenetic library development files

rec: [libbpp-phyl-omics-dev]

Bio++ Phylogenetics library: genomics components (development files)

rec: [libbpp-popgen-dev]

Bio++ Population Genetics library development files

rec: [libbpp-qt-dev]

Bio++ Qt Graphic classes library development files

rec: [libbpp-raa-dev]

Bio++ Remote Acnuc Access library development files

rec: [libbpp-seq-dev]

Bio++ Sequence library development files

rec: [libbpp-seq-omics-dev]

Bio++ Sequence library: genomics components (development files)

rec: [libcdk-java]

Chemistry Development Kit (CDK) Java libraries

rec: [libchado-perl]

database schema and tools for genomic data

rec: [libcifpp-dev]

Documentation for libcifpp

rec: [libconsensuscore-dev]

algorithms for PacBio multiple sequence consensus -- development files

rec: [libdivsufsort-dev]

libdivsufsort header files

rec: [libedlib-dev]

library for sequence alignment using edit distance (devel)

rec: [libfast5-dev]

library for reading Oxford Nanopore Fast5 files -- headers

rec: [libfastahack-dev]

library for indexing and sequence extraction from FASTA files (devel)

rec: [libffindex0-dev]

library for simple index/database for huge amounts of small files (development)

rec: [libfml-dev]

development headers for libfml

rec: [libgatbcore-dev]

development library of the Genome Analysis Toolbox

rec: [libgclib-dev]

header files for Genome Code Lib (GCLib)

rec: [libgenome-dev]

toolkit for developing bioinformatic related software (devel)

rec: [libgenome-model-tools-music-perl]

module for finding mutations of significance in cancer

rec: [libgenome-perl]

pipelines, tools, and data management for genomics

rec: [libgenometools0-dev]

development files for GenomeTools

rec: [libgff-dev]

GFF/GTF parsing from cufflinks as a library

rec: [libgkarrays-dev]

library to query large collection of NGS sequences (development)

rec: [libgo-perl]

perl modules for GO and other OBO ontologies

rec: [libhdf5-dev]

HDF5 - development files - serial version

rec: [libhmsbeagle-dev]

High-performance lib for Bayesian and Maximum Likelihood phylogenetics (devel)

rec: [libhts-dev]

development files for the HTSlib

rec: [libhtscodecs-dev]

Development headers for custom compression for CRAM and others

rec: [libhtsjdk-java]

Java API for high-throughput sequencing data (HTS) formats

rec: [libjebl2-java]

Java Evolutionary Biology Library

rec: [libjloda-java]

Java library of data structures and algorithms for bioinformatics

rec: [libkmer-dev]

suite of tools for DNA sequence analysis (development lib)

rec: [libmems-dev]

development library to support DNA string matching and comparative genomics

rec: [libminimap2-dev]

development headers for libminimap

rec: [libmuscle-dev]

multiple alignment development library for protein sequences

rec: [libncbi-vdb-dev]

libraries for using data in the INSDC Sequence Read Archives (devel)

rec: [libncbi6-dev]

NCBI libraries for biology applications (development files)

rec: [libncl-dev]

NEXUS Class Library (static lib and header files)

rec: [libngs-java]

Next Generation Sequencing language Bindings (Java bindings)

rec: [libnhgri-blastall-perl]

Perl extension for running and parsing NCBI's BLAST 2.x

rec: [libopenmm-dev]

C++ header files for the OpenMM library

rec: [libopenms-dev]

library for LC/MS data management and analysis - dev files

rec: [libpal-java]

Phylogenetic Analysis Library

rec: [libparasail-dev]

Development heaaders and static libraries for parasail

rec: [libpbbam-dev]

Pacific Biosciences binary alignment/map (BAM) library (headers)

rec: [libpbdata-dev]

tools for handling PacBio sequences (development files)

rec: [libpbihdf-dev]

tools for handling PacBio hdf5 files (development files)

rec: [libpbseq-dev]

library for analyzing PacBio sequencing data (development files)

rec: [libpdb-redo-dev]

Development files for libpdb-redo

rec: [libpll-dev]

Phylogenetic Likelihood Library (development)

rec: [libqes-dev]

DNA sequence parsing library -- development

rec: [librcsb-core-wrapper0-dev]

development files for librcsb-core-wrapper0t64

rec: [librdp-taxonomy-tree-java]

taxonomy tree library from Ribosomal Database Project (RDP)

rec: [librg-blast-parser-perl]

very fast NCBI BLAST parser - binding for Perl

rec: [librg-reprof-bundle-perl]

protein secondary structure and accessibility predictor (perl module)

rec: [librostlab-blast0-dev]

very fast C++ library for parsing the output of NCBI BLAST programs (devel)

rec: [librostlab3-dev]

C++ library for computational biology (development)

rec: [libsbml5-dev]

System Biology Markup Language library - development files

rec: [libseqan2-dev]

C++ library for the analysis of biological sequences (development)

rec: [libseqan3-dev]

C++ library for the analysis of biological sequences v3 (development)

rec: [libseqlib-dev]

C++ htslib/bwa-mem/fermi interface for interrogating sequence data (dev)

rec: [libslow5-dev]

header and static library for reading & writing SLOW5 files

rec: [libsmithwaterman-dev]

determine similar regions between two strings or genomic sequences (devel)

rec: [libsnp-sites1-dev]

Static libraries and header files for the package snp-sites

rec: [libsort-key-top-perl]

Perl module to select and sort top n elements of a list

rec: [libspoa-dev]

SIMD partial order alignment library (development files)

rec: [libsrf-dev]

C++ implementation of the SRF format for DNA sequence data

rec: [libssm-dev]

macromolecular superposition library - development files

rec: [libssu-dev]

high-performance phylogenetic diversity calculations (dev)

rec: [libssw-dev]

Development headers and static libraries for libssw

rec: [libssw-java]

Java bindings for libssw

rec: [libstaden-read-dev]

development files for libstaden-read

rec: [libstatgen-dev]

development files for the libStatGen

rec: [libswiss-perl]

Perl API to the UniProt database

rec: [libtabixpp-dev]

C++ wrapper to tabix indexer (development files)

rec: [libthread-pool-dev]

C++ header-only thread pool library (devel)

rec: [libvcflib-dev]

C++ library for parsing and manipulating VCF files (development)

rec: [libvibrant6-dev]

NCBI libraries for graphic biology applications (development files)

rec: [libwfa2-dev]

exact gap-affine algorithm (development)

rec: [libzerg-perl]

fast perl module for parsing the output of NCBI BLAST programs

rec: [libzerg0-dev]

development libraries and header files for libzerg

rec: [mcl]

Markov Cluster algorithm

rec: [ont-fast5-api]

simple interface to HDF5 files of the Oxford Nanopore .fast5 file format

rec: [pyfai]

Fast Azimuthal Integration scripts

rec: [python3-airr]

Data Representation Standard library for antibody and TCR sequences

rec: [python3-bcbio-gff]

Python3 library to read and write Generic Feature Format

rec: [python3-bioframe]

library to enable flexible, scalable operations on genomic interval dataframes

rec: [python3-biom-format]

Biological Observation Matrix (BIOM) format (Python 3)

rec: [python3-biomaj3]

BioMAJ workflow management library

rec: [python3-biopython]

Python3 library for bioinformatics

rec: [python3-biotools]

Python3 bioinformatics utilities for high-throughput genomic sequencing

rec: [python3-bx]

library to manage genomic data and its alignment

rec: [python3-cgecore]

Python3 module for the Center for Genomic Epidemiology

rec: [python3-cigar]

manipulate SAM cigar strings

rec: [python3-cooler]

library for a sparse, compressed, binary persistent storage

rec: [python3-corepywrap]

library that exports C++ mmCIF accessors to Python3

rec: [python3-csb]

Python framework for structural bioinformatics (Python3 version)

rec: [python3-cutadapt]

Clean biological sequences from high-throughput sequencing reads (Python 3)

rec: [python3-cyvcf2]

VCF parser based on htslib (Python 3)

rec: [python3-deeptools]

platform for exploring biological deep-sequencing data

rec: [python3-deeptoolsintervals]

handlig GTF-like sequence-associated interal-annotation

rec: [python3-dendropy]

DendroPy Phylogenetic Computing Library (Python 3)

rec: [python3-dnaio]

Python 3 library for fast parsing of FASTQ and FASTA files

rec: [python3-ete3]

Python Environment for (phylogenetic) Tree Exploration - Python 3.X

rec: [python3-fast5]

library for reading Oxford Nanopore Fast5 files -- Python 3

rec: [python3-freecontact]

fast protein contact predictor - binding for Python3

rec: [python3-gfapy]

flexible and extensible software library for handling sequence graphs

rec: [python3-gffutils]

Work with GFF and GTF files in a flexible database framework

rec: [python3-gtfparse]

parser for gene transfer format (aka GFF2)

rec: [python3-htseq]

Python3 high-throughput genome sequencing read analysis utilities

rec: [python3-intervaltree-bio]

Interval tree convenience classes for genomic data -- Python 3 library

rec: [python3-kineticstools]

detection of DNA modifications (Python 3 library)

rec: [python3-mirtop]

annotate miRNAs with a standard mirna/isomir naming (Python 3)

rec: [python3-nanoget]

extract information from Oxford Nanopore sequencing data and alignments

rec: [python3-ngs]

Next Generation Sequencing language Bindings (Python3 bindings)

rec: [python3-pairix]

1D/2D indexing and querying with a pair of genomic coordinates

rec: [python3-pangolearn]

store of the trained model for pangolin to access

rec: [python3-parasail]

Python3 bindings for the parasail C library

rec: [python3-pbcommand]

common command-line interface for Pacific Biosciences analysis modules

rec: [python3-pbconsensuscore]

algorithms for PacBio multiple sequence consensus -- Python 3

rec: [python3-pbcore]

Python 3 library for processing PacBio data files

rec: [python3-peptidebuilder]

generate atomic oligopeptide 3D structure from sequence

rec: [python3-presto]

toolkit for processing B and T cell sequences (Python3 module)

rec: [python3-propka]

heuristic pKa calculations with ligands (Python 3)

rec: [python3-py2bit]

access to 2bit files

rec: [python3-pyabpoa]

adaptive banded Partial Order Alignment - python3 module

rec: [python3-pyani]

Python3 module for average nucleotide identity analyses

rec: [python3-pybedtools]

Python 3 wrapper around BEDTools for bioinformatics work

rec: [python3-pybel]

Biological Expression Language

rec: [python3-pybigwig]

Python 3 module for quick access to bigBed and bigWig files

rec: [python3-pyfaidx]

efficient random access to fasta subsequences for Python 3

rec: [python3-pyfastx]

fast random access to sequences from FASTA/Q file - python3 module

rec: [python3-pymummer]

Python 3 interface to MUMmer

rec: [python3-pyranges]

2D representation of genomic intervals and their annotations

rec: [python3-pysam]

interface for the SAM/BAM sequence alignment and mapping format (Python 3)

rec: [python3-pyspoa]

Python bindings to spoa

rec: python3-pyvcf

Package not available

rec: [python3-rdkit]

Collection of cheminformatics and machine-learning software

rec: [python3-ruffus]

Python3 computation pipeline library widely used in bioinformatics

rec: [python3-screed]

short nucleotide read sequence utils in Python 3

rec: [python3-shasta]

nanopore whole genome assembly (dynamic library)

rec: [python3-skbio]

Python3 data structures, algorithms, educational resources for bioinformatic

rec: [python3-slow5]

Python3 modul for reading & writing SLOW5 files

rec: [python3-sqt]

SeQuencing Tools for biological DNA/RNA high-throughput data

rec: [python3-streamz]

build pipelines to manage continuous streams of data

rec: [python3-tinyalign]

numerical representation of differences between strings

rec: [python3-torch]

Tensors and Dynamic neural networks in Python (Python Interface)

rec: [python3-treetime]

inference of time stamped phylogenies and ancestral reconstruction (Python 3)

rec: [python3-unifrac]

high-performance phylogenetic diversity calculations

rec: [python3-wdlparse]

Workflow Description Language (WDL) parser for Python

rec: [r-bioc-biobase]

base functions for Bioconductor

rec: [r-cran-boolnet]

assembling, analyzing and visualizing Boolean networks

rec: [r-cran-corrplot]

Visualization of a Correlation Matrix

rec: [r-cran-distory]

GNU R distance between phylogenetic histories

rec: [r-cran-fitdistrplus]

support fit of parametric distribution

rec: [r-cran-forecast]

GNU R forecasting functions for time series and linear models

rec: [r-cran-genetics]

GNU R package for population genetics

rec: [r-cran-gprofiler2]

Interface to the 'g:Profiler' Toolset

rec: [r-cran-haplo.stats]

GNU R package for haplotype analysis

rec: [r-cran-phangorn]

GNU R package for phylogenetic analysis

rec: [r-cran-pheatmap]

GNU R package to create pretty heatmaps

rec: [r-cran-phylobase]

GNU R base package for phylogenetic structures and comparative data

rec: [r-cran-pscbs]

R package: Analysis of Parent-Specific DNA Copy Numbers

rec: [r-cran-qqman]

R package for visualizing GWAS results using Q-Q and manhattan plots

rec: [r-cran-rentrez]

GNU R interface to the NCBI's EUtils API

rec: [r-cran-rncl]

GNU R interface to the Nexus Class Library

rec: [r-cran-rnexml]

GNU R package for semantically rich I/O for the 'NeXML' format

rec: [r-cran-rotl]

GNU R interface to the 'Open Tree of Life' API

rec: [r-cran-samr]

GNU R significance analysis of microarrays

rec: [r-cran-sctransform]

Variance Stabilizing Transformations for Single Cell UMI Data

rec: [r-cran-seqinr]

GNU R biological sequences retrieval and analysis

rec: [r-cran-seurat]

Tools for Single Cell Genomics

rec: [r-cran-tsne]

t-distributed stochastic neighbor embedding for R (t-SNE)

rec: [r-cran-vegan]

Community Ecology Package for R

rec: [r-cran-webgestaltr]

find over-represented properties in gene lists

rec: [ruby-bio]

Ruby tools for computational molecular biology

rec: [ruby-crb-blast]

Run conditional reciprocal best blast

rec: [sbmltoolbox]

libsbml toolbox for octave and matlab

rec: [snakemake]

pythonic workflow management system

rec: [toil]

cross-platform workflow engine

sug: bioclipse

Package not available

sug: [capsule-nextflow]

packaging and deployment tool for Java applications

sug: [conda-package-handling]

create and extract conda packages of various formats

sug: [ctdconverter]

Convert CTD files into Galaxy tool and CWL CommandLineTool files

sug: [cthreadpool-dev]

minimal ANSI C thread pool - development files

sug: [cwlformat]

code formatter for Common Workflow Language

sug: [cwltest]

Common Workflow Language testing framework

sug: [libargs-dev]

simple header-only C++ argument parser library

sug: libatomicqueue-dev

Package not available

sug: [libbam-dev]

manipulates nucleotide sequence alignments in BAM or SAM format

sug: [libbbhash-dev]

bloom-filter based minimal perfect hash function library

sug: [libbifrost-dev]

static library and header files for libbifrost

sug: [libbiojava4-java]

Java API to biological data and applications (default version)

sug: [libbiosoup-dev]

C++ header-only support library for bioinformatics tools

sug: [libbtllib-dev]

Bioinformatics Technology Lab common code library

sug: [libcapsule-maven-nextflow-java]

packaging tool for Java applications with Maven coordinates

sug: [libconcurrentqueue-dev]

industrial-strength lock-free queue for C++

sug: [libdisorder-dev]

library for entropy measurement of byte streams (devel)

sug: libfast-perl

Package not available

sug: libforester-java

Package not available

sug: [libfreecontact-dev]

fast protein contact predictor library - development files

sug: [libfreecontact-doc]

documentation for libfreecontact

sug: [libfreecontact-perl]

fast protein contact predictor - binding for Perl

sug: [libgatk-bwamem-java]

interface to call Heng Li's bwa mem aligner from Java code

sug: [libgatk-bwamem-jni]

interface to call Heng Li's bwa mem aligner from Java code (jni)

sug: [libgatk-fermilite-java]

interface to call Heng Li's fermi-lite assembler from Java code

sug: [libgatk-fermilite-jni]

interface to call Heng Li's fermi-lite assembler from Java code (jni)

sug: [libgatk-native-bindings-java]

library of native bindings for gatk and picard-tools

sug: libgenomicsdb-dev

Package not available

sug: libgenomicsdb-java

Package not available

sug: [libicb-utils-java]

Java library of utilities to manage files and compute statistics

sug: [libmaus2-dev]

collection of data structures and algorithms for biobambam (devel)

sug: [libmilib-java]

library for Next Generation Sequencing (NGS) data processing

sug: [libminimap-dev]

development headers for libminimap

sug: libmmblib-dev

Package not available

sug: [libmodhmm-dev]

library for constructing, training and scoring hidden Markov models (dev)

sug: libnexml-java

Package not available

sug: libngs-sdk-dev

Package not available

sug: [libpbcopper-dev]

data structures, algorithms, and utilities for C++ applications -- header files

sug: libpwiz-dev

Package not available

sug: libqcpp-dev

Package not available

sug: librelion-dev

Package not available

sug: libroadrunner-dev

Package not available

sug: [librostlab-blast-doc]

very fast C++ library for parsing the output of NCBI BLAST programs (doc)

sug: [librostlab-doc]

C++ library for computational biology (documentation)

sug: [libsavvy-dev]

C++ interface for the SAV file format

sug: [libsuma-dev]

headers and static library for sumatra and sumaclust

sug: [libsvmloc-dev]

PSORTb adapted library for svm machine-learning library (dev)

sug: libswarm2-dev

Package not available

sug: [libterraces-dev]

enumerate terraces in phylogenetic tree space (development lib)

sug: [libtfbs-perl]

scanning DNA sequence with a position weight matrix

sug: [libvbz-hdf-plugin-dev]

VBZ compression plugin for nanopore signal data (devel)

sug: [libxxsds-dynamic-dev]

succinct and compressed fully-dynamic data structures library

sug: nim-hts-dev

Package not available

sug: nim-kexpr-dev

Package not available

sug: nim-lapper-dev

Package not available

sug: octace-bioinfo

Package not available

sug: [python-biopython-doc]

Documentation for the Biopython library

sug: [python3-alignlib]

edit and Hamming distances for biological sequences

sug: python3-anndata

Package not available

sug: python3-bcbio

Package not available

sug: [python3-bel-resources]

Python3 utilities for BEL resource files

sug: [python3-bioblend]

CloudMan and Galaxy API library (Python 3)

sug: [python3-biopython-sql]

Biopython support for the BioSQL database schema (Python 3)

sug: [python3-cgelib]

Python3 code to be utilized across the CGE tools

sug: python3-cobra

Package not available

sug: python3-cogent3

Package not available

sug: python3-compclust

Package not available

sug: [python3-conda-package-streaming]

fetch conda metadata

sug: python3-consensuscore2

Package not available

sug: [python3-ctdopts]

Gives your Python tools a CTD-compatible interface

sug: python3-galaxy-lib

Package not available

sug: python3-intake

Package not available

sug: [python3-joypy]

ridgeline-/joyplots plotting routine

sug: [python3-loompy]

access loom formatted files for bioinformatics

sug: python3-misopy

Package not available

sug: [python3-ncls]

datastructure for interval overlap queries

sug: [python3-networkx]

tool to create, manipulate and study complex networks (Python3)

sug: [python3-pycosat]

Python bindings to picosat

sug: python3-pyflow

Package not available

sug: python3-roadrunner

Package not available

sug: python3-scanpy

Package not available

sug: [python3-seqcluster]

analysis of small RNA in NGS data

sug: q2-alignment

Package not available

sug: q2-composition

Package not available

sug: q2-cutadapt

Package not available

sug: q2-dada2

Package not available

sug: q2-deblur

Package not available

sug: q2-demux

Package not available

sug: q2-diversity

Package not available

sug: q2-emperor

Package not available

sug: q2-feature-classifier

Package not available

sug: q2-feature-table

Package not available

sug: q2-fragment-insertion

Package not available

sug: q2-gneiss

Package not available

sug: q2-longitudinal

Package not available

sug: q2-metadata

Package not available

sug: q2-phylogeny

Package not available

sug: q2-quality-control

Package not available

sug: q2-quality-filter

Package not available

sug: q2-sample-classifier

Package not available

sug: q2-shogun

Package not available

sug: q2-taxa

Package not available

sug: q2-types

Package not available

sug: q2-vsearch

Package not available

sug: q2cli

Package not available

sug: q2cwl

Package not available

sug: q2lint

Package not available

sug: [q2templates]

Design template package for QIIME 2 Plugins

sug: qiime

Package not available

sug: [r-bioc-affxparser]

Affymetrix File Parsing SDK

sug: [r-bioc-affy]

BioConductor methods for Affymetrix Oligonucleotide Arrays

sug: [r-bioc-affyio]

BioConductor tools for parsing Affymetrix data files

sug: [r-bioc-altcdfenvs]

BioConductor alternative CDF environments

sug: [r-bioc-annotate]

BioConductor annotation for microarrays

sug: [r-bioc-annotationdbi]

GNU R Annotation Database Interface for BioConductor

sug: [r-bioc-annotationhub]

GNU R client to access AnnotationHub resources

sug: [r-bioc-aroma.light]

BioConductor methods normalization and visualization of microarray data

sug: [r-bioc-arrayexpress]

access to the ArrayExpress Microarray Database at EBI

sug: [r-bioc-biocgenerics]

generic functions for Bioconductor

sug: [r-bioc-biocneighbors]

Nearest Neighbor Detection for Bioconductor Packages

sug: [r-bioc-biomart]

GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)

sug: [r-bioc-biomformat]

GNU R interface package for the BIOM file format

sug: [r-bioc-biostrings]

GNU R string objects representing biological sequences

sug: [r-bioc-biovizbase]

GNU R basic graphic utilities for visualization of genomic data

sug: r-bioc-bitseq

Package not available

sug: r-bioc-bridgedbr

Package not available

sug: [r-bioc-bsgenome]

BioConductor infrastructure for Biostrings-based genome data packages

sug: r-bioc-cager

Package not available

sug: [r-bioc-cner]

CNE Detection and Visualization

sug: [r-bioc-complexheatmap]

make complex heatmaps using GNU R

sug: [r-bioc-ctc]

Cluster and Tree Conversion

sug: [r-bioc-cummerbund]

tool for analysis of Cufflinks RNA-Seq output

sug: [r-bioc-dada2]

sample inference from amplicon sequencing data

sug: [r-bioc-deseq2]

R package for RNA-Seq Differential Expression Analysis

sug: [r-bioc-dnacopy]

R package: DNA copy number data analysis

sug: [r-bioc-ebseq]

R package for RNA-Seq Differential Expression Analysis

sug: r-bioc-enrichedheatmap

Package not available

sug: [r-bioc-ensembldb]

GNU R utilities to create and use an Ensembl based annotation database

sug: [r-bioc-genefilter]

methods for filtering genes from microarray experiments

sug: [r-bioc-geneplotter]

R package of functions for plotting genomic data

sug: [r-bioc-genomeinfodb]

BioConductor utilities for manipulating chromosome identifiers

sug: [r-bioc-genomicalignments]

BioConductor representation and manipulation of short genomic alignments

sug: [r-bioc-genomicfeatures]

GNU R tools for making and manipulating transcript centric annotations

sug: [r-bioc-genomicranges]

BioConductor representation and manipulation of genomic intervals

sug: [r-bioc-geoquery]

Get data from NCBI Gene Expression Omnibus (GEO)

sug: [r-bioc-go.db]

annotation maps describing the entire Gene Ontology

sug: [r-bioc-graph]

handle graph data structures for BioConductor

sug: [r-bioc-gseabase]

Gene set enrichment data structures and methods

sug: [r-bioc-gsva]

Gene Set Variation Analysis for microarray and RNA-seq data

sug: [r-bioc-gviz]

Plotting data and annotation information along genomic coordinates

sug: [r-bioc-hypergraph]

BioConductor hypergraph data structures

sug: [r-bioc-impute]

Imputation for microarray data

sug: [r-bioc-iranges]

GNU R low-level containers for storing sets of integer ranges

sug: [r-bioc-limma]

linear models for microarray data

sug: [r-bioc-makecdfenv]

BioConductor CDF Environment Maker

sug: [r-bioc-mergeomics]

Integrative network analysis of omics data

sug: [r-bioc-metagenomeseq]

GNU R statistical analysis for sparse high-throughput sequencing

sug: [r-bioc-mofa]

Multi-Omics Factor Analysis (MOFA)

sug: [r-bioc-multiassayexperiment]

Software for integrating multi-omics experiments in BioConductor

sug: r-bioc-nanostringqcpro

Package not available

sug: [r-bioc-oligo]

Preprocessing tools for oligonucleotide arrays

sug: [r-bioc-oligoclasses]

Classes for high-throughput arrays supported by oligo and crlmm

sug: [r-bioc-org.hs.eg.db]

genome-wide annotation for Human

sug: [r-bioc-pcamethods]

BioConductor collection of PCA methods

sug: [r-bioc-phyloseq]

GNU R handling and analysis of high-throughput microbiome census data

sug: [r-bioc-preprocesscore]

BioConductor collection of pre-processing functions

sug: [r-bioc-purecn]

copy number calling and SNV classification using targeted short read sequencing

sug: [r-bioc-qusage]

qusage: Quantitative Set Analysis for Gene Expression

sug: [r-bioc-rbgl]

R interface to the graph algorithms contained in the BOOST library

sug: r-bioc-rentrez

Package not available

sug: [r-bioc-rsamtools]

GNU R binary alignment (BAM), variant call (BCF), or tabix file import

sug: [r-bioc-rtracklayer]

GNU R interface to genome browsers and their annotation tracks

sug: [r-bioc-s4vectors]

BioConductor S4 implementation of vectors and lists

sug: [r-bioc-savr]

GNU R parse and analyze Illumina SAV files

sug: [r-bioc-shortread]

GNU R classes and methods for high-throughput short-read sequencing data

sug: [r-bioc-snpstats]

BioConductor SnpMatrix and XSnpMatrix classes and methods

sug: [r-bioc-structuralvariantannotation]

Variant annotations for structural variants

sug: [r-bioc-tfbstools]

GNU R Transcription Factor Binding Site (TFBS) Analysis

sug: [r-bioc-titancna]

Subclonal copy number and LOH prediction from whole genome sequencing

sug: [r-bioc-tximport]

transcript-level estimates for biological sequencing

sug: [r-bioc-variantannotation]

BioConductor annotation of genetic variants

sug: [r-bioc-xvector]

BioConductor representation and manpulation of external sequences

sug: [r-cran-adegenet]

GNU R exploratory analysis of genetic and genomic data

sug: [r-cran-adephylo]

GNU R exploratory analyses for the phylogenetic comparative method

sug: [r-cran-amap]

Another Multidimensional Analysis Package

sug: [r-cran-biwt]

biweight mean vector and covariance and correlation

sug: r-cran-drinsight

Package not available

sug: [r-cran-dt]

GNU R wrapper of the JavaScript library 'DataTables'

sug: [r-cran-dynamictreecut]

Methods for Detection of Clusters in Hierarchical Clustering

sug: [r-cran-fastcluster]

Fast hierarchical clustering routines for GNU R

sug: [r-cran-future.apply]

apply function to elements in parallel using futures

sug: [r-cran-future.batchtools]

Future API for Parallel and Distributed Processing

sug: [r-cran-ica]

Independent Component Analysis

sug: [r-cran-itertools]

Iterator Tools

sug: [r-cran-kaos]

Encoding of Sequences Based on Frequency Matrix Chaos

sug: [r-cran-metap]

Meta-Analysis of Significance Values

sug: [r-cran-minerva]

Maximal Information-Based Nonparametric Exploration

sug: [r-cran-natserv]

GNU R 'NatureServe' Interface

sug: [r-cran-nmf]

GNU R framework to perform non-negative matrix factorization

sug: [r-cran-optimalcutpoints]

Computing Optimal Cutpoints in Diagnostic Tests

sug: [r-cran-parmigene]

Parallel Mutual Information to establish Gene Networks

sug: [r-cran-pcapp]

Robust PCA by Projection Pursuit

sug: [r-cran-proc]

Display and Analyze ROC Curves

sug: [r-cran-rann]

Fast Nearest Neighbour Search Using L2 Metric

sug: [r-cran-rcpphnsw]

R bindings for a Library for Approximate Nearest Neighbors

sug: [r-cran-robustrankaggreg]

Methods for robust rank aggregation

sug: [r-cran-rocr]

GNU R package to prepare and display ROC curves

sug: [r-cran-rook]

web server interface for R

sug: [r-cran-rsvd]

Randomized Singular Value Decomposition

sug: [r-cran-shazam]

Immunoglobulin Somatic Hypermutation Analysis

sug: [r-cran-sitmo]

GNU R parallel pseudo random number generator 'sitmo' header files

sug: [r-cran-venndiagram]

Generate High-Resolution Venn and Euler Plots

sug: r-other-apmswapp

Package not available

sug: [ruby-rgfa]

parse, edit and write GFA format graphs in Ruby

sug: [vdjtools]

framework for post-analysis of B/T cell repertoires