bioconda / packages

Package Name Access Summary Updated
perl-pod-usage public print a usage message from embedded pod documentation 2022-05-21
mg-toolkit public Metagenomics toolkit. 2022-05-21
scglue public Graph-linked unified embedding for unpaired single-cell multi-omics data integration 2022-05-21
pcaone public PCAone - Principal Component Analysis All in One 2022-05-21
chronumental public Make time trees from large phylogenetic divergence trees 2022-05-21
cwltest public Common workflow language testing framework 2022-05-21
perl-xml-xpath public Parse and evaluate XPath statements. 2022-05-21
pyega3 public EGA python client 2022-05-21
perl-compress-raw-zlib public Basic utilities for writing tests. 2022-05-21
perl-xml-libxslt public Interface to GNOME libxslt library 2022-05-21
pasa public PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments. 2022-05-21
msmetaenhancer public MSMetaEnhancer is a Python tool that adds more annotations (e.g. SMILES, InChI, CAS number) to MSP files. 2022-05-21
recognizer public A tool for domain based annotation with the COG database 2022-05-21
lrphase public Phasing individual long reads using known haplotype information. 2022-05-21
famsa public Algorithm for large-scale multiple sequence alignments 2022-05-21
perl-math-bigrat public Arbitrary big rational numbers 2022-05-21
hesslab-gambit public Tool for rapid taxonomic identification of microbial pathogens 2022-05-21
gget public gget enables efficient querying of genomic databases 2022-05-21
abyss public Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler 2022-05-21
pyrodigal public Python bindings to Prodigal, an ORF finder for microbial sequences. 2022-05-21
methylartist public Tools for parsing and plotting nanopore methylation data 2022-05-21
jbrowse2 public The JBrowse 2 Genome Browser 2022-05-21
constax public A software for accurate taxonomic classification of environmental DNA markers 2022-05-21
fec public An error correction tool 2022-05-21
coidb public A tool to obtain and maintain a database of COI metabarcode references 2022-05-21
manta public Structural variant and indel caller for mapped sequencing data 2022-05-20
msstitch public MS proteomics post processing utilities 2022-05-20
r-conos public Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB. 2022-05-20
svdb public structural variant database software 2022-05-20
autometa public Automated extraction of genomes from shotgun metagenomes 2022-05-20
expam public Metagenomic profiling using a reference phylogeny 2022-05-20
liquorice public A tool for bias correction and quantification of changes in coverage around regions of interest in cfDNA WGS datasets 2022-05-20
dnarrange public Find rearrangements in "long" DNA reads relative to a genome sequence 2022-05-20
taxonkit public A Cross-platform and Efficient NCBI Taxonomy Toolkit 2022-05-20
gtdbtk public A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. 2022-05-20
clair3 public Clair3 is a small variant caller for long-reads. Compare to PEPPER (r0.4), Clair3 (v0.1) shows a better SNP F1-score with ≤30-fold of ONT data (precisionFDA Truth Challenge V2), and a better Indel F1-score, while runs generally four times faster. Clair3 makes the best of both worlds of using pileup or full-alignment as input for deep-learning based long-read small variant calling. Clair3 is simple and modular for easy deployment and integration. 2022-05-20
coinfinder public A tool for the identification of coincident (associating and dissociating) genes in pangenomes. 2022-05-19
pegasusio public PegasusIO is the IO package for Pegasus. 2022-05-19
aprfinder public Tool for finding aphased repeats. 2022-05-19
perl-svg public Perl extension for generating Scalable Vector Graphics (SVG) documents 2022-05-19
refgenconf public A standardized configuration object for reference genome assemblies 2022-05-19
poseidon-xerxes public A tool (xerxes) to analyse genotype databases formatted using Poseidon. 2022-05-19
isoquant public IsoQuant is a tool for reference-based analysis of long RNA reads. 2022-05-19
breakfast public breakfast: fast putative outbreak cluster and infection chain detection using SNPs 2022-05-19
kaiju public Fast and sensitive taxonomic classification for metagenomics 2022-05-19
syri public Synteny and rearrangement identifier between whole-genome assemblies 2022-05-19
auspice public Auspice is an open-source interactive tool for visualising phylogenomic data 2022-05-19
augustus public AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments. 2022-05-19
last public LAST finds & aligns related regions of sequences. 2022-05-19
seqscreen public SeqScreen was created to sensitively assign taxonomic classifications, functional annotations, and biological processes of interest to single, short DNA sequences (50bp-1,000bp). 2022-05-19

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