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bioconda / packages

Package Name Access Summary Updated
flash2 public Merge paired-end reads from fragments that are shorter than twice the read length 2024-12-11
plass public Plass (Protein-Level ASSembler) and PenguiN (Protein-guided Nucleotide assembler) are methods to assemble short read sequencing data on a protein level to proteins or DNA contigs 2024-12-11
perl-config-any public Load configuration from different file formats, transparently 2024-12-11
mdasim public This is MDAsim 2+, a tool to simulate whole genome amplification of a DNA sequence with multiple displacement amplification. A citation for this version will be provided when available. MDAsim 2+ extends MDAsim 1.2, so please also always cite: Tagliavi Z, Draghici S. MDAsim: A multiple displacement amplification simulator. 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2012. pp. 1–4. doi:10.1109/BIBM.2012.6392622 2024-12-11
ucsc-hubpubliccheck public checks that the labels in hubPublic match what is in the hub labels 2024-12-11
sparseassembler public No Summary 2024-12-11
ucsc-gtftogenepred public convert a GTF file to a genePred 2024-12-11
mageck public MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data. 2024-12-11
perl-tie-hash-indexed public Ordered hashes for Perl 2024-12-11
mummer4 public MUMmer is a system for rapidly aligning entire genomes 2024-12-11
r2r public software to speed depiction of aesthetic consensus RNA secondary structures 2024-12-11
heinz public The algorithm for identification of the optimal scoring subnetwork. 2024-12-11
perl-filesys-df public Perl extension for filesystem disk space information. 2024-12-11
famseq public Peng G, Fan Y, Palculict TB, Shen P, Ruteshouser EC, Chi A, Davis RW, Huff V, Scharfe C, Wang W. Rare variant detection using family-based sequencing analysis. Proceedings of the National Academy of Sciences. 2013 Mar 5;110(10):3985-90 2024-12-11
rnaz public predicting structural noncoding RNAs 2024-12-11
ucsc-genepredtobiggenepred public converts genePred or genePredExt to bigGenePred input (bed format with extra fields) 2024-12-11
hardklor public Analyze mass spectra 2024-12-11
ucsc-checkcoveragegaps public Check for biggest gap in coverage for a list of tracks. 2024-12-11
debwt public A efficient method to construct BWT index of a given DNA sequence, especially useful for gigantic and high similar genome. DeBWT has good scalability to construct BWT in parallel computing. It is well-suited to run on multiple core servers or clusters to construct the BWT of large collections of genome sequences. 2024-12-11
verifybamid public No Summary 2024-12-11
ucsc-bamtopsl public Convert a bam file to a psl and optionally also a fasta file that contains the reads. 2024-12-11
mentalist public The MLST pipeline developed by the PathOGiST research group. 2024-12-11
mbuffer public mbuffer is a tool for buffering data streams with a large set of unique features 2024-12-11
comet-ms public Comet is a command line tool that does MS/MS database search. 2024-12-11
ucsc-hgloadbed public Load a generic bed file into database 2024-12-11
ucsc-mafcoverage public Analyse coverage by maf files - chromosome by 2024-12-11
ucsc-hgloadoutjoined public load new style (2014) RepeatMasker .out files into database 2024-12-11
rainbow public Efficient tool for clustering and assembling short reads, especially for RAD 2024-12-11
ucsc-liftup public change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf 2024-12-11
treebest public TreeBeST: Tree Building guided by Species Tree, used in the Ensembl Compara pipeline. 2024-12-11
gmtk public A publicly available toolkit for rapidly prototyping statistical models using dynamic graphical models (DGMs) and dynamic Bayesian networks (DBNs) 2024-12-11
r-epic public Estimate the Proportion of Immune and Cancer cells from bulk gene expression data. 2024-12-11
ucsc-bedintersect public Intersect two bed files 2024-12-11
genesplicer public No Summary 2024-12-11
ucsc-genepredsinglecover public create single-coverage genePred files 2024-12-11
ucsc-parasync public uses paraFetch to recursively mirror url to given path 2024-12-11
ncrf public Noise-Cancelling Repeat Finder, Uncovering tandem repeats in error-prone long-read sequencing data. 2024-12-11
gnu-wget public No Summary 2024-12-11
ucsc-validatefiles public Validates the format of different genomic files. 2024-12-11
r-gwpcr public Implements the necessary distributions and parameter estimation procedures for a model of amplification and high-troughput sequencing. The model is based on a mechanistic model of PCR amplification as a Galton-Watson branching process, and on Poissonan sampling to model high-throughput sequencing. 2024-12-11
msisensor public MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline. 2024-12-11
extract-sv-reads public Tool for extracting splitter or discordant reads from a BAM or CRAM file. 2024-12-11
plink public Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. 2024-12-11
prophasm public ProPhasm – ProPhyle Assembler. Compressing k-mer sets via assembling contigs. 2024-12-11
extract_fullseq public extract_fullseq is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets 2024-12-11
ucsc-lavtopsl public Convert blastz lav to psl format 2024-12-11
filtlong public Filtlong is a tool for filtering long reads. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. 2024-12-11
mgs-canopy public No Summary 2024-12-11
ucsc-bigwigtobedgraph public Convert from bigWig to bedGraph format. 2024-12-11
htsbox public HTSbox is a fork of early HTSlib. It is a collection of small experimental tools manipulating HTS-related files. 2024-12-11

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