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MCView creates a Shiny app facilitating interactive exploration and annotation of Metacell models.
scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.
This package provides the reference implementation of CGP workflow for CaVEMan SNV analysis.
The Spliced Transcripts Alignment to a Reference (STAR) software is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.
This package provides a subset of the Regulatory Sequence Analysis Tools (RSAT).
This package provides in uncompressed version of the gnomAD structural variant sites.
This package contains a collection of bioinformatics data structures and algorithms. It provides I/O classes, bitio classes, text indexing classes and BAM sequence alignment functionality.
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files are formated appropriately
This package provides software for phylogenomic inference.
The CodeMin minimization library provides a set of lightweight minimization functions originally developed for the CodeAxe phylogenetic analysis package.
hiddenDomains is a suite of programs used to identify significant enrichment of ChIP-seq reads that span large domains, like HK27me3. The input data can be in BAM format, or in a tab-delimited 'reads per bin' format described below. The output is a BED formatted file the lists the enriched domains and their posterior probabilities.
MetaMaps is tool specifically developed for the analysis of long-read (PacBio/Oxford Nanopore) metagenomic datasets.
This module provides code coverage metrics for Perl. Code coverage metrics describe how thoroughly tests exercise code. By using Devel::Cover you can discover areas of code not exercised by your tests and determine which tests to create to increase coverage.
This package provides a tool to extract assembly statistics from FASTA and FASTQ files.
This package provides an interface for the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. This includes interfaces to blastn, blastp, blastx, and makeblastdb.
Build contrasts for models defined with formulaic.
This package is used to apply filtering on raw VCF calls generated using CaVEMan.
This packages provides a collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.