bioconda / packages

Package Name Access Summary Updated
fusioncatcher public Finder of Somatic Fusion Genes in RNA-seq data. 2019-02-17
scanpy public Single-Cell Analysis in Python. Scales to >1M cells. 2019-02-16
anndata public An annotated data matrix. 2019-02-16
tango public Assign taxonomy to metagenomic contigs using blastx searches 2019-02-16
mykrobe public Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. 2019-02-16
kaiju public Fast and sensitive taxonomic classification for metagenomics 2019-02-16
whatshap public phase genomic variants using DNA sequencing reads (haplotype assembly) 2019-02-16
sina public Reference based multiple sequence alignment 2019-02-16
isocor public A Isotope Correction for mass spectrometry labeling experiments 2019-02-16
rapid public Read Alignment, Analysis, and Differential Pipeline (RAPID) is a set of tools for the alignment, and analysis of genomic regions with small RNA clusters derived from small RNA sequencing data. 2019-02-16
moff public moFF is an OS independent tool designed to extract apex MS1 intensity using a set of identified MS2 peptides. 2019-02-15
fusioncatcher-seqtk public This is modified Seqtk version required for FusionCatcher. 2019-02-15
umis public Tools for processing UMI RNA-tag data 2019-02-15
ataqv public ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing. 2019-02-15
compare-reads public cythonized function to compare reads by name. 2019-02-15
jbrowse public The JBrowse Genome Browser 2019-02-15
kipoi_veff public kipoi_veff: variant effect prediction plugin for Kipoi 2019-02-15
shapeshifter public A tool for managing and transforming large data sets 2019-02-15
snakemake public Snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style. Snakemake workflows are essentially Python scripts extended by declarative code to define rules. Rules describe how to create output files from input files. This package provides the full installation including all optional dependencies. 2019-02-15
gromacs public GROMACS is a versatile package to perform molecular dynamics. 2019-02-15
snakemake-minimal public Snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style. Snakemake workflows are essentially Python scripts extended by declarative code to define rules. Rules describe how to create output files from input files. This package provides the core snakemake functionility. For features like reports and remote files, check out the snakemake package which provides all optional dependencies. 2019-02-15
maxbin2 public MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. 2019-02-15
digestiflow-cli public Command line client for Digestiflow. 2019-02-15
infernal public Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. 2019-02-15
wg-blimp public wg-blimp (Whole Genome BisuLfIte sequencing Methylation analysis Pipeline) can be utilised to analyse WGBS data. It performs alignment, qc, methylation calling, DMR calling and DMR annotation using a multitude of tools. 2019-02-15
sniffles public Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore) 2019-02-15
pbccs public pbccs - Generate Accurate Consensus Sequences from a Single SMRTbell 2019-02-15
stream public STREAM Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data http://stream.pinellolab.org 2019-02-15
staramr public Scan genome contigs against the ResFinder and PointFinder databases 2019-02-15
deeptoolsintervals public A python module creating/accessing GTF-based interval trees with associated meta-data 2019-02-14
arb-bio-devel public ARB 6 Sequence Analysis Suite 2019-02-14
arb-bio public ARB 6 Sequence Analysis Suite 2019-02-14
arb-bio-tools public ARB 6 Sequence Analysis Suite 2019-02-14
libarbdb public ARB 6 Sequence Analysis Suite 2019-02-14
fpa public Filter Pairwise Alignment filter long read mapping information to save disk space 2019-02-14
socru public Order and orientation of complete bacterial genomes 2019-02-14
r-basejump public Base functions for bioinformatics and R package development. 2019-02-14
seurat-scripts public A set of wrappers for individual components of the Seurat 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. 2019-02-14
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
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