microPIECE - microRNA pipeline enhanced by CLIP experiments - v1.5.2

• Refactoring of CLIP_merge_bed_files.pl to reduce memory footprint by a factor of 10x (Fixes #174)
• Refactoring of Piranha run to support multithreading (Fixes #177)
• Fixing copy process of final files (Fixes #184)
• Setting default bin size for Piranha to 30 (Fixes #178)
• This version is archived as .

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - v1.5.1 Performance improvements

Added optimized pre-binning step for Piranha (Fixes #132)

This version is archived as .

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - v1.2.3 Single matures for precursor

• Fix transformation of precursor sequences based on mirbase #22 precursor sequences with a single mature (Fixes L<#109|https://github.com/microPIECE-team/microPIECE/issues/109>)

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - v1.3.0 mirBase dat-file as source for mature/precursor sequences

• Creating all structures on the fly using pseudo-mirBASE-dat as input.
• Using miRNA.dat from mirBASE as source for mature/precursor sequence and relationship (Fixes #127)
• Fix of division-by-zero bug for empty mapping files (Fixes #118)
• Fix of typo in --piranhabinsize option (Fixes #116)

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - v1.5.0 Accepted version of microPIECE (including some improvements)

• Removing additional length cutoff during CLIP transfer (Fixes #153)
  • Add command line options --CLIPminProcessLength, --CLIPmaxProcessLength, and --CLIPminlength for length limits used in run_CLIP_process and run_CLIP_clip_mapper steps enabling processing of peaks with user defined widths (Fixes #145)
• Dynamic naming of output files based on minlength variable in run_CLIP_clip_mapper (Fixes #146)
• Correct calculation of length of a bed feature and moving scripts/CLIP_bedtool_discard_sizes.pl into lib/microPIECE.pm (Fixes #147)
• Add an optimized pre-binning step with pseudocounts for bins covered by an exon as preparation for Piranha (Fixes #132 and #155)
• This version is archived as .
• This version was accepted by The Journal of Open Source Software (Review issue #616)

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - v1.4.0 Pseudo mirBASE files and structures

• Copying pseudo mirBASE dat file final_mirbase_pseudofile.dat into output folder (Fixes #131)
• Corrected RNA::HairpinFigure output (Fixes #137)
• Fix the requirement of an accession inside mirBASE dat file (Fixes #134)
• Avoiding error message while copying the out file for genomic location into base folder (Fixes #117)

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - Reenable miraligner

Downgrades java inside docker container to version 1.7.*, due to miraligner requirement.

Fixes #97 and #98

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - Improved collision handling for newly miRNAs stable IDs

Improved collision detection for newly identified miRNAs avoiding crashed caused by genomic copies. (Fixes #105)

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - Stable IDs for newly identified miRNAs

Enables stable numbering for newly identified miRNAs based on their precursor and mature sequences

Fixes #101

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - v1.1.0 isomirs and genomic location

Add isomir detection and copy the final genomic location file to the output filter

Fixes #34

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - v1.0.7 Add Piranah bin size parameter

Piranha step was lacking of a bin_size parameter. Added parameter --piranahbinsize with a default value of 20.

Fixes #80

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - v1.0.6 Local mirbase directory and relocation of temporary files

Added parameter --mirbasedir and --tempdir to support local mirbase files and relocation of directory for temporary files (Fixes #66, #73, and #76)

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - v1.0.5 Correct documentation for --mirna parameter

Update of documentation and correct spelling of --mirna parameter

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - v1.0.4 Completed miRNAs in final mining output

Fixes missing complete mature in final output (Fixes #69)

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - v1.0.3 Adding tests for BED issues

Add tests for perl scripts in script folder which ensure the correct handling of BED stop coordinates (Fixes #65)

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - v1.0.2 BED sorting fixed

Fixes the incorrect sorting of BED files, result was correct, but sorting was performed in the wrong order. (Fixes #63)

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - v1.0.1 BED stop handling part I

Fix an error conserning BED file handling of start and stop coordinates. (Fixes #59)

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - v1.0.0 Submission to JOSS

Archived as and submitted to The Journal of Open Source Software.

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago

microPIECE - microRNA pipeline enhanced by CLIP experiments - v0.9.0 First public release

This is the first public release and it is archived at Zenodo with the

Scientific Software - Peer-reviewed - Perl
Published by greatfireball almost 8 years ago