Skip to content

1 News

Jump to bottom Edit New page
Nuno Fonseca edited this page Oct 1, 2018 · 9 revisions

News about iRAP.

  • 01/10/2018 - Release 1.0.0. Several fixes and changes related tp the single-cell analysis. Upgraded multiple external software packages (e.g., htseq, salmon, featurecounts, fastq_utils, star, ...).
  • 13/03/2018 - Release 1.0.0a. New major (alpha) release. New: support for single-cell RNA-seq (smart-seq2, drop-seq, 10X, ...). Several fixes and performance improvements in iRAP's code, update of 3rd party tools (e.g., mappers, quantification tools). iRAP now follows semantic versioning (https://semver.org/).
  • 09/01/2018 - Release 0.8.5p8 DESeq and DESeq2: support quantification matrices with floats.
  • 27/11/2017 - Release 0.8.5p7 Fix issue #36. Changed install script: OSA aligner is no longer installed by default (it may still be installed with the -x option available in irap_install.sh ) .
  • 08/09/2017 - Release 0.8.5p3 Fixed bug in irap_single_lib where a few files were not being copied to the final folder. Other minor changes.
  • 11/05/2017 - Release 0.8.5p2 Fix: issue #28
  • 27/04/2017 - Release 0.8.5p1 Bug fix: fixed a failure that occured in debian based distros due to the use of the rename command.
  • 23/03/2017 - Release 0.8.5. Bug fixes. Improved support for transcript quantification: generation of relative isoform usage and dominant transcripts. Star support: more flexible parameter customization.
  • 20/01/2017 - Release 0.8.3. Improved support for large genomes (big_genome=y option); bowtie2 upgrade; minor fixes.
  • 14/12/2016 - Release 0.8.2. Several fixes, performance improvements, and 3rd party upgrades. New: initial support for Salmon and HISAT2.
  • 16/02/2016 - Release 0.8.0a. New release with upgraded version of different tools. Several fixes and performance improvements in iRAP code. Improved installation script (more flexible and with less dependencies). Docker images available for Fedora and Ubuntu. Support for new quantification methods: kallisto, RSEM, and StringTie. Added support for gene fusion analysis (current method supported is FusionMap). Note that since it is a major new release it is not fully backwards compatible to version 0.7.x.
  • 19/03/2015 - Moving to GitHub.
  • 15/03/2015 - Release 0.6.1. Several fixes and initial support for DESeq2.
  • 03/03/2015 - Release 0.6.0. New: iRAP docker images and wrappers; options to add read group ids and arbitrary sam headers to BAM files; BAM statistics reports (faster and more detailed). Upgraded versions of several tools and packages.
  • 20/10/2014 - Release 0.5.0. New: support for MapSplice and NURD; initial input files (FASTQ/BAM) can now be distributed across different sub-folders; support for strand-specific RNA-seq data (<libname>_strand parameter); upgraded versions of many tools (TopHat, Cufflinks, Bowtie, ...).
  • 14/06/2014 - Release 0.4.2. Several fixes and improvements (mostly in the report generation).
  • 06/06/2014 - Manuscript describing iRAP available in [http://biorxiv.org/content/early/2014/06/06/005991 bioRxiv].
  • 02/05/2014 - Release 0.4.0. Include support for gene set enrichment (GSE) analysis. Web report generation for all stages of the analysis (QC, mapping, quantification, DE and GSE) - in beta status. Improved installation script and support for manual (semi-automatic) installation.
  • 08/01/2014 - Release 0.3.3. Several fixes and improvements. Upgrade of 3rd party tools to more recent versions.
  • 26/11/2013 - Release 0.3.0 Several fixes and improvements. BAM support: accept BAM files as input (as an alternative for FASTQ files). RPKMs: generate tsv files with RPKMs per feature/library.
  • 21/08/2013 - iRAP is now online.
Add a custom footer
Clone this wiki locally