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Repository alevin
Name: alevin
Owner: bgruening
Synopsis: Alevin function from the salmon
Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves
 is accuracy and speed via a number of different innovations, including the use of quasi-mapping (accurate but fast-to-compute proxies for
 traditional read alignments), and massively-parallel stochastic collapsed variational inference. The result is a versatile tool that fits
 nicely into many differnt pipelines. For example, you can choose to make use of our quasi-mapping algorithm by providing Salmon with raw
 sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. an unsorted BAM file produced with
 your favorite aligner), and it will use the same wicked-fast, state-of-the-art inference algorithm to estimate transcript-level abundances
 for your experiment. Alevin adds to this functionality with a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing
 data, performing cell barcode detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell
 barcode whitelisting.
Type: unrestricted
Revision: 1:c0ea43315baf
This revision can be installed: True
Times cloned / installed: 959

Repository README files - may contain important installation or license information

Galaxy wrappers for salmon ===================================== These wrappers are copyright 2014, updated 2018 by Björn Grüning, Mhd Ramez Alrawas and additional contributors. All rights reserved. See the licence text below. Currently tested with salmon 0.11.2. Automated Installation ====================== Galaxy should be able to automatically install the salmon for you if you have Conda dependency management enabled in Galaxy. For more information please read the documentation at: History ======= ======== ====================================================================== Version Changes -------- ---------------------------------------------------------------------- v0.6.3.0 - First release -------- ---------------------------------------------------------------------- v0.7.2 - Second release -------- ---------------------------------------------------------------------- v0.8.2 - Third release -------- ---------------------------------------------------------------------- v0.9.1 - Fourth release -------- ---------------------------------------------------------------------- v0.11.2 - Fifth release ======== ====================================================================== Bug Reports =========== You can file an issue here or ask us on the Galaxy development list Licence (MIT) ============= Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Contents of this repository

Name Description Version Minimum Galaxy Version
Quantification and analysis of 3’ tagged-end single-cell sequencing data 0.14.1 16.01

Sequence Analysis - Tools for performing Protein and DNA/RNA analysis
RNA - Utilities for RNA
Transcriptomics - Tools for use in the study of Transcriptomics.