bioconda / packages

Package Name Access Summary Updated
r2r public software to speed depiction of aesthetic consensus RNA secondary structures 2018-09-24
phylip public Package of programs for inferring phylogenies 2018-09-24
truvari public Structural variant comparison tool for VCFs 2018-09-24
cnvkit public Copy number variant detection from high-throughput sequencing 2018-09-24
weeder public No Summary 2018-09-24
star public An RNA-seq read aligner. 2018-09-24
thermorawfileparser public Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono 2018-09-24
nanocomp public Comparing runs of Oxford Nanopore sequencing data and alignments 2018-09-23
nanostat public Calculate statistics for Oxford Nanopore sequencing data and alignments 2018-09-23
nanoplot public Plotting suite for long read sequencing data and alignments 2018-09-23
nanoqc public Create fastQC-like plots for Oxford Nanopore sequencing data 2018-09-23
nanoget public Functions to extract information from Oxford Nanopore sequencing data and alignments. 2018-09-23
nanoplotter public Plotting functions of Oxford Nanopore sequencing data for NanoPack 2018-09-23
haystack_bio public Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline 2018-09-23
ectyper public ECTyper is a python program for serotyping E. coli genomes 2018-09-23
bioconductor-cardinal public Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification. 2018-09-23
bioconductor-biobase public Functions that are needed by many other packages or which replace R functions. 2018-09-23
bioconductor-matter public Memory-efficient reading, writing, and manipulation of structured binary data on disk as vectors, matrices, and arrays. 2018-09-23
bioconductor-biocgenerics public S4 generic functions needed by many Bioconductor packages. 2018-09-23
bioconductor-protgenerics public S4 generic functions needed by Bioconductor proteomics packages. 2018-09-23
planemo public Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/). 2018-09-23
galaxy-lib public Subset of Galaxy (http://galaxyproject.org/) core code base designed to be used a library. 2018-09-23
vqsr_cnn public Variant quality score recalibration with Convolutional Neural Networks 2018-09-22
gatktool public Functions and classes used to extend a GATK tool with Python 2018-09-22
gatk4 public Genome Analysis Toolkit (GATK4) 2018-09-22
duphold public SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. 2018-09-22
abeona public A simple transcriptome assembler based on kallisto and Cortex graphs. 2018-09-22
metaxa public Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data. 2018-09-21
flowcraft public A Nextflow pipeline assembler for genomics. Pick your modules. Assemble them. Run the pipeline. 2018-09-21
maker public MAKER is a portable and easily configurable genome annotation pipeline. 2018-09-21
cortexpy public A Python API for manipulating (Mc)Cortex de novo assembly graph and link data 2018-09-21
r-metstat public A diverse collection of metabolomics related statistical tools. 2018-09-21
smeg public Strain-level MEtagenomic Growth estimation (SMEG) measures growth rates of microbial strains from complex metagenomic dataset at low coverage (1X) 2018-09-21
r-popgenome public Provides efficient tools for population genomics data analysis, able to process individual loci, large sets of loci, or whole genomes. PopGenome <DOI:10.1093/molbev/msu136> not only implements a wide range of population genetics statistics, but also facilitates the easy implementation of new algorithms by other researchers. PopGenome is optimized for speed via the seamless integration of C code. 2018-09-20
r-blockfest public An R implementation of an extension of the 'BayeScan' software (Foll, 2008) <DOI:10.1534/genetics.108.092221> for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection. 2018-09-20
delly public Structural variant discovery by integrated paired-end and split-read analysis 2018-09-20
bcbio-nextgen-vm public Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines 2018-09-20
bcbio-nextgen public Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis 2018-09-20
slamdunk public SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis. 2018-09-20
fastani public FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). 2018-09-20
sina public SINA is a tool for aligning sequences with an existing multiple sequence alignment (MSA) at high accuracy. It can also execute a homology search based on the computed alignment and generate a per sequence classifications from the search results. 2018-09-20
reparation_blast public a pipeline that uses ribosome profiling data for a de novo open reading frame delineation in prokaryotic (bacterial) genomes. I changed the original reparation project to use the open-source blast tool (https://blast.ncbi.nlm.nih.gov/Blast.cgi) instead of the commercial usearch --ublast tool (https://drive5.com/usearch/manual/ublast_algo.html). I did this in order to add this tool to bioconda without having licensing issues with the commercial usearch -ublast tool. The original software was created at VIB-UGent Center for Medical Biotechnology and Lab of Bioinformatics and Computational Genomics (Biobix), University of Gent, Belgium, by Elvis Ndah. (https://github.com/Biobix/REPARATION). Be advised that the adapted version has slightly different results and is slower than the original reparation software. 2018-09-20
bowtie2 public Fast and sensitive read alignment 2018-09-20
blast public BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit. 2018-09-20
evidencemodeler public Evidence Modeler combines ab intio gene predictions, protein alignments, and transcript alignments into weighted consensus gene structures 2018-09-20
biolib public Package for common tasks in bioinformatic. 2018-09-19
peptide-shaker public PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data! 2018-09-19
genenotebook public A colleborative notebook for genes and genomes 2018-09-19
kraken2 public Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. 2018-09-19
ascat public ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy (Figure 1). ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour cell, expressed as multiples of haploid genomes) from SNP array or massively parallel sequencing data, and calculates whole-genome allele-specific copy number profiles (the number of copies of both parental alleles for all SNP loci across the genome). 2018-09-19
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