Enter the query into the form above. You can look for specific version of a package by using @ symbol like this: gcc@10.
API method:
GET /api/packages?search=hello&page=1&limit=20
where search is your query, page is a page number and limit is a number of items on a single page. Pagination information (such as a number of pages and etc) is returned
in response headers.
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python-cwl-utils provides python utilities and autogenerated classes for loading and parsing CWL v1.0, CWL v1.1, and CWL v1.2 documents.
This package contains some tools for processing BAM files including:
bamsormadup: parallel sorting and duplicate marking
bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name
bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field
bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column
bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading.
bamsort: reads BAM and writes BAM resorted by coordinates or query name
bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name.
Taxtastic is software written in python used to build and maintain reference packages i.e. collections of reference trees, reference alignments, profiles, and associated taxonomic information.
Mosaicatcher counts Strand-seq reads and classifies strand states of each chromosome in each cell using a Hidden Markov Model.
Flexbar preprocesses high-throughput nucleotide sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.
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.
PyLiftover is a library for quick and easy conversion of genomic (point) coordinates between different assemblies.
Python scripts to find enrichment of GO terms. In addition, this package is used for processing the obo-formatted file from Gene Ontology website. The data structure is a directed acyclic graph that allows easy traversal from leaf to root.
GSEApy is a Python/Rust implementation for GSEA and wrapper for Enrichr. GSEApy can be used for RNA-seq, ChIP-seq, Microarray data. It can be used for convenient GO enrichment and to produce publication quality figures in Python.
PiGx is a collection of genomics pipelines. It includes the following pipelines:
PiGx BSseq for raw fastq read data of bisulfite experiments
PiGx RNAseq for RNAseq samples
PiGx scRNAseq for single cell dropseq analysis
PiGx ChIPseq for reads from ChIPseq experiments
All pipelines are easily configured with a simple sample sheet and a descriptive settings file. The result is a set of comprehensive, interactive HTML reports with interesting findings about your samples.
Biopython is a set of tools for biological computation including parsers for bioinformatics files into Python data structures; interfaces to common bioinformatics programs; a standard sequence class and tools for performing common operations on them; code to perform data classification; code for dealing with alignments; code making it easy to split up parallelizable tasks into separate processes; and more.
This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.
Infernal ("INFERence of RNA ALignment") is a tool for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.
This is a set of R functions that allows you to generate precise figures. This tool will create clean markdown reports about what you just discovered.
GNU Bison is a general-purpose parser generator. It can build a deterministic or generalized LR parser from an annotated, context-free grammar. It is versatile enough to have many applications, from parsers for simple tools through complex programming languages.
Bison also provides an implementation of yacc, as specified by POSIX.
GNU Bison is a general-purpose parser generator. It can build a deterministic or generalized LR parser from an annotated, context-free grammar. It is versatile enough to have many applications, from parsers for simple tools through complex programming languages.
Bison also provides an implementation of yacc, as specified by POSIX.
Stig is a TUI and CLI client for the BitTorrent client Transmission.
qBittorrent Enhanced is a bittorrent client based on qBittorrent with the following features:
Auto Ban Xunlei, QQ, Baidu, Xfplay, DLBT and Offline downloader
Auto Ban Unknown Peer from China Option (Default: OFF)
Auto Update Public Trackers List (Default: OFF)
Auto Ban BitTorrent Media Player Peer Option (Default: OFF)
Peer whitelist/blacklist
uGet is portable download manager with GTK+ interface supporting HTTP, HTTPS, BitTorrent and Metalink, supporting multi-connection downloads, download scheduling, download rate limiting.
LibTorrent is a BitTorrent library used by and developed in parallel with the BitTorrent client rtorrent. It is written in C++ with emphasis on speed and efficiency.
qBittorrent Enhanced is a bittorrent client based on qBittorrent with the following features:
Auto Ban Xunlei, QQ, Baidu, Xfplay, DLBT and Offline downloader
Auto Ban Unknown Peer from China Option (Default: OFF)
Auto Update Public Trackers List (Default: OFF)
Auto Ban BitTorrent Media Player Peer Option (Default: OFF)
Peer whitelist/blacklist
qBittorrent Enhanced is a bittorrent client based on qBittorrent with the following features:
Auto Ban Xunlei, QQ, Baidu, Xfplay, DLBT and Offline downloader
Auto Ban Unknown Peer from China Option (Default: OFF)
Auto Update Public Trackers List (Default: OFF)
Auto Ban BitTorrent Media Player Peer Option (Default: OFF)
Peer whitelist/blacklist
Tremc is a console client, with a curses interface, for the Transmission BitTorrent daemon.
Transmission is a BitTorrent client that comes with graphical, textual, and Web user interfaces. Transmission also has a daemon for unattended operations. It supports local peer discovery, full encryption, DHT, µTP, PEX and Magnet Links.