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Biosoup is a C++ collection of header-only data structures used for storage and logging in bioinformatics tools.
This package lets you read and write files in Generic Feature Format (GFF) with Biopython integration.
Mosaicatcher counts Strand-seq reads and classifies strand states of each chromosome in each cell using a Hidden Markov Model.
This package provides a toolbox to process, analyze and visualize spatial single-cell expression data.
ngshmmalign is a profile HMM aligner for NGS reads designed particularly for small genomes (such as those of RNA viruses like HIV-1 and HCV) that experience substantial biological insertions and deletions.
Zarr backend for DelayedArray objects.
This package provides Python bindings for lib2bit to access 2bit files with Python.
This program compares version strings. It intends to be a replacement for strverscmp.
Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files.
ctxcore is part of the SCENIC suite of tools. It provides core functions for pycisTarget and SCENIC.
Picard is a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats. Picard is implemented using the HTSJDK Java library to support accessing file formats that are commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and VCF.
This package provides a convenient interface to minimap2, a fast and accurate C program to align genomic and transcribe nucleotide sequences.
EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq analysis tool Scanpy (Genome Biology, 2018).
TopHat is a fast splice junction mapper for nucleotide sequence reads produced by the RNA-Seq method. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
Entrez Direct (EDirect) is a method for accessing the National Center for Biotechnology Information's (NCBI) set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a terminal. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions.
PiGx BSseq is a data processing pipeline for raw fastq read data of bisulfite experiments; it produces reports on aggregate methylation and coverage and can be used to produce information on differential methylation and segmentation.
The alignment module of BioJava provides an API that contains
implementations of dynamic programming algorithms for sequence alignment;
reading and writing of popular alignment file formats;
a single-, or multi- threaded multiple sequence alignment algorithm.
This package provides data for the book "Computational Genomics with R".
Bio::Kseq provides ruby bindings to the kseq.h FASTA and FASTQ parsing code. It provides a fast iterator over sequences and their quality scores.
This package offers Cython bindings and a Python interface for Prodigal. Prodigal is an ORF finder designed for both genomes and metagenomes.
This package provides an accurate VCF/GFF3/GTF LiftOver tool for new genome assemblies.
This package is designed to streamline scATAC analyses in R.
The HH-suite is a software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
This package provides a toolkit for measuring and comparing ATAC-seq results. It was written to make it easier to spot differences that might be caused by ATAC-seq library prep or sequencing. The main program, ataqv, examines aligned reads and reports some basic metrics.