bioconda / packages

Package Name Access Summary Updated
mafft public Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform 2021-07-25
aquilasv public A region-based diploid assembly and variants calling tool 2021-07-25
lotus2 public LotuS2 is a lightweight complete 16S/18S/ITS pipeline 2021-07-24
sdm public sdm - simple demultiplex tool for FASTQ demultiplexing and dereplication 2021-07-24
dadaist2 public Command line wrapper to run DADA2 on a set of paired-end reads 2021-07-24
deepsignal-plant public A deep-learning method for detecting DNA methylation state from Oxford Nanopore sequencing reads of plants 2021-07-24
irida-staramr-results public IRIDA StarAMR Results program enables StarAMR analysis results that were run through IRIDA to be batch downloaded into a collection of spreadsheets using the command line. 2021-07-24
clair3-illumina public Clair3 with libraries to support variant calling using Illumina short-reads. Version in sync with Clair3. 2021-07-24
aquila_sv public Diploid assembly and variants calling tool 2021-07-24
phanotate public Phanotate gene caller for phages 2021-07-24
isoquant public IsoQuant is a tool for reference-based analysis of long RNA reads. 2021-07-24
pango-designation public Repository for suggesting new lineages that should be added to the current 2021-07-24
aplanat public Bokeh plotting API, with bio-focussed extras. 2021-07-24
tb-profiler public Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data 2021-07-24
ultraplex public fastq demultiplexer 2021-07-24
spades public SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies. 2021-07-23
serotypefinder public SerotypeFinder identifies the serotype in total or partial sequenced isolates of E. coli. 2021-07-23
python-bioext public A few handy bioinformatics tools not already in BioPython 2021-07-23
r-bcbiornaseq public R package for bcbio RNA-seq analysis. 2021-07-23
cellprofiler public CellProfiler is free, open-source software for quantitative analysis of biological images 2021-07-23
atlas-gene-annotation-manipulation public Scripts for manipulating gene annotation 2021-07-23
ostir public Open Source Transcription Initiation Rates 2021-07-23
kipoi-utils public kipoi-utils: utils used in various packages related to kipoi 2021-07-23
treeswift public TreeSwift: Fast tree module for Python 2 and 3 2021-07-23
dxpy public DNAnexus Platform API bindings for Python 2021-07-23
ptools_bin public Installation for ptools scripts. 2021-07-23
sscocaller public Haplotyping single-cell DNA sequenced gamete cells. 2021-07-23
synapseclient public Python client for Synapse 2021-07-23
r-signac public A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart and Butler et al. (2019) <doi:10.1016/j.cell.2019.05.031>. 2021-07-23
r-sigminer public Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2020) <DOI:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Macintyre, Geoff, et al. (2018) <DOI:10.1038/s41588-018-0179-8>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study. 2021-07-23
arvados-python-client public Python API for Arvados 2021-07-23
jcvi public Python utility libraries on genome assembly, annotation and comparative genomics 2021-07-23
planemo public Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/). 2021-07-23
trim-galore public Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control 2021-07-23
salmon public Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment 2021-07-23
das_tool public Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. 2021-07-23
alevin-fry public alevin-fry is a tool for the efficient processing of single-cell data based on RAD files produced by alevin 2021-07-22
deepbgc public DeepBGC - Biosynthetic Gene Cluster detection and classification 2021-07-22
cellprofiler-core public Dependency for CellProfiler v4 2021-07-22
r-acidplots public Functions for plotting genomic data. 2021-07-22
trust4 public TCR and BCR assembly from bulk or single-cell RNA-seq data 2021-07-22
tasmanian-mismatch public Tasmanian tool to analyze mismatches at read and position in high throughput sequencing data 2021-07-22
varlociraptor public Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control. 2021-07-22
r-acidmarkdown public Toolkit for extending the functionality of R Markdown. 2021-07-22
chewbbaca public A complete suite for gene-by-gene schema creation and strain identification. 2021-07-22
scanpy-scripts public Scripts for using scanpy from the command line 2021-07-22
miru-hero public Compute MIRU and Spoligotype from a M. tuberculosis genome 2021-07-22
methyldackel public A (mostly) universal methylation extractor for BS-seq experiments. Formerly named PileOMeth. 2021-07-22
scirpy public A Scanpy extension for analyzing single-cell T-cell receptor sequencing data. 2021-07-22
dragonflye public Microbial assembly pipeline for Nanopore reads 2021-07-22

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