bioconda / packages

Package Name Access Summary Updated
ucsc-cell-browser public A browser for single-cell data, main site at http://cells.ucsc.edu 2019-02-13
spydrpick public Mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure 2019-02-13
biobb_model public Biobb_model is the Biobb module collection to check and model 3d structures, create mutations or reconstruct missing atoms. 2019-02-13
r-syntactic public Make syntactically valid names out of character vectors. This package is part of the basejump toolkit. 2019-02-13
r-brio public Biological R input/output. This package is part of the basejump toolkit. 2019-02-13
msp2db public Python package to create an SQLite database from a collection of MSP mass spectromertry spectra files. Currently works with MSP files formated as MassBank records or as MoNA records. The resulting SQLite database can be used for spectral matching with msPurity Bioconductor R package, 2019-02-13
slamdunk public SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis. 2019-02-13
npinv public an accurate tool for detecting and genotyping inversion using multiple alignment long reads 2019-02-13
trumicount public For NGS experiments using unique molecular identifiers (UMIs), molecules that are lost entirely during sequencing cause under- estimation of the molecule count, and amplification artifacts like PCR chimeras cause over-estimation. TRUmiCount corrects UMI data for both types of errors, thus improving the accuracy of measured molecule counts considerably. 2019-02-13
python-omero public Client library offering helper methods to access an OMERO server. 2019-02-13
umi_tools public Tools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs) 2019-02-13
ucsc-gtftogenepred public convert a GTF file to a genePred 2019-02-13
ucsc-genepredtogtf public Convert genePred table or file to gtf. 2019-02-13
ucsc-genepredtobed public Convert from genePred to bed format. Does not yet handle genePredExt 2019-02-13
ucsc-fatotwobit public Convert DNA from fasta to 2bit format 2019-02-13
ucsc-bedtogenepred public convert bed format files to genePred format 2019-02-13
hisat2 public graph-based alignment of next generation sequencing reads to a population of genomes 2019-02-13
bioconductor-rhdf5 public This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM. 2019-02-13
bioconductor-rhdf5lib public Provides C and C++ hdf5 libraries. 2019-02-13
bcbio-variation-recall public Parallel merging, squaring off and ensemble calling for genomic variants 2019-02-13
arvados-python-client public Python API for Arvados, an open source platform for managing and analyzing biomedical big data 2019-02-13
graphaligner public Sequence to graph aligner for long reads 2019-02-13
svim public SVIM is a structural variant caller for long reads. 2019-02-13
r-transformer public Additional S3 and S4 coercion methods for easy interconversion between Bioconductor and tidyverse data classes. This package is part of the basejump toolkit. 2019-02-13
bwa public The BWA read mapper. 2019-02-13
fmlrc public A long-read error correction tool using the multi-string Burrows Wheeler Transform 2019-02-13
r-goalie public Assertive check functions for defensive R programming. goalie is an attempt to incorporate elements of multiple assertive check packages into a single package with as few dependencies as possible. All assertive checks are written in the most basic R code possible, without reliance on compilation (e.g. C++/Rcpp). It is still a work in progress, and feature requests are welcome. 2019-02-12
r-bioverbs public S4 generic functions for bioinformatics, part of the basejump toolkit. 2019-02-12
tximport-scripts public A set of wrappers for individual components of the tximport package. Functions R packages are hard to call when building workflows outside of R, so this package adds a set of simple wrappers with robust argument parsing. Intermediate steps are currently mainly serialized R objects, but the ultimate objective is to have language-agnostic intermediate formats allowing composite workflows using a variety of software packages. 2019-02-12
mztosqlite public Convert proteomics data files into a SQLite database. 2019-02-11
pythonnet public No Summary 2019-02-11
cromwell public A Workflow Management System geared towards scientific workflows described in WDL 2019-02-10
stream_atac public STREAM-Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data. Preprocessing steps for single cell atac-seq data. 2019-02-10
arvados-cwl-runner public Arvados Common Workflow Language runner 2019-02-10
intarna public Efficient RNA-RNA interaction prediction incorporating seeding and accessibility of interacting sites 2019-02-09
cnv_facets public Detect somatic copy number variants (CNV) in tumour-normal samples using next generation sequencing data 2019-02-09
stacks public Stacks is a software pipeline for building loci from RAD-seq 2019-02-09
dammet public Software to reconstruct methylomes from HTS data underlying and ancient specimen 2019-02-09
perl-text-levenshtein public calculate the Levenshtein edit distance between two strings 2019-02-09
viennarna public Vienna RNA package -- RNA secondary structure prediction and comparison 2019-02-09
vawk public An awk-like VCF parser 2019-02-09
openms public OpenMS is an open-source software C++ library for LC-MS data management and analyses 2019-02-09
hicap public In silico typing of the H. influenzae capsule locus 2019-02-08
hicexplorer public Set of programs to process, analyze and visualize Hi-C data 2019-02-08
minnow public A principled framework for rapid simulation of dscRNA-seq data at the read level 2019-02-08
pourrna public Compute local minima and respective transition rates of an RNA energy landscape. 2019-02-08
abeona public A simple transcriptome assembler based on kallisto and Cortex graphs. 2019-02-08
hicmatrix public Library to manage Hi-C matrices for HiCExplorer and pyGenomeTracks 2019-02-08
subread public High-performance read alignment, quantification, and mutation discovery 2019-02-08
star public An RNA-seq read aligner. 2019-02-08
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