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@tjakobi tjakobi released this Aug 17, 2020

We are proud to release a new major version of circtools, 1.2.0 as of today.

Highlights

  • 1.2.0 features the new siRNA design module that allows to design siRNAs that can be used to knock-down specific circRNAs
  • circtools 1.2.0 requires Python >= 3.6 (due to Biopython)
  • Both, DCC and FUCHS have been ported to Python 3.5 and will not work with Python 2.x anymore.

Fixes

  • 1.2.0 contains general bugfixes
  • Fix broken pysam dependency of HTseq for DCC #58
  • Adding python package reportlab to dependency list
  • Updated install procedure
  • Fixing Read the Docs build error
  • Fixing failing Travis tests
  • Primex crashes when product length > circRNA length #75
  • primex script no validates input parameters for the PCR product size
  • Adding -n flag for specifying the number of primer pairs (default: 10)
  • Implementing curl macOS fix for #77
  • circtools installation sets wrong R library folder in .Renviron #78
  • Error using R version 3.6 #76
  • Updating bedtools version to 2.29.2
  • Updating R dependencies
  • Adding sus scrofa support for primex
Assets 2

@tjakobi tjakobi released this Feb 27, 2019 · 91 commits to master since this release

We are proud to release the new version of circtools, 1.1.0.8 as of today.

Changes

  • 1.1.0.8 contains several bug fixes general bugfixes
  • #72 has been fixed, setting the correct default value for the enrichment module
  • #70 has been addressed, fixing the broken formatter of the primer design output
  • Fixing broken --help switch
  • Adding rat blasting support for primex
  • quickcheck module: changing log scale labeling to 10^x view
  • reconstruct module: adding significance bars to all suitable plots
  • circtest module: re-introducing orphan circRNA length plots
Assets 2

@tjakobi tjakobi released this Oct 1, 2018 · 107 commits to master since this release

We are proud to release the new version of circtools, 1.1.0.7 as of today.

Resolved code issues

  • 1.1.0.4 contains several bug fixes regarding the installation process, namely missing depencies for statsmodels
  • An error relating to pysam and HTSeq during from-scratch installations of DCC has been solved
  • Empty lines in DCC input files no longer result in incorrect behavior (Issue #64)
  • The enrich module's help entry for -c incorrectly referred to the circRNACount file while it should be the
    CircCoordinates

Resolved / improved documentation issues

  • The documentation now clearly states the Python2 dependency of DCC and FUCHS (Issue #60)
    • NOTE: DCC and FUCHS are right now tested with Python3, therefore the installation process will be more straightforward in upcoming releases
  • The documentation now uses consistent Python3 versions (Issue #61)
  • The documentation of the enrich module was updated with a background section (Issue #62)
  • The documentation was completely overhauled and now consistently uses one data set for all analyses (Issue #25 )
  • STAR and StringTie are now listed as dependencies int the documentation (Issue #66)
  • The documentation now uses publicly usable HTTPS git links (Issue #65)
Assets 2

@tjakobi tjakobi released this Aug 3, 2018 · 155 commits to master since this release

Solved issues

  • 1.1.0.6 is a bugfix release that fixes a broken symlink within the exon module
Assets 2

@tjakobi tjakobi released this Aug 3, 2018 · 157 commits to master since this release

Solved issues

  • 1.1.0.4a is a bugfix release that fixes a legacy column from the circtest module for use within the exon module
Assets 2

@tjakobi tjakobi released this Aug 3, 2018 · 160 commits to master since this release

We are proud to release the new version of circtools, 1.1.0.4 as of today.

Solved issues

  • 1.1.0.4 is a bugfix release that addresses a missing installation dependency (scipi) to the setup process
Assets 2
Pre-release

@tjakobi tjakobi released this Aug 3, 2018 · 157 commits to master since this release

Solved issues

  • 1.1.0.4a is a bugfix release that fixes a legacy column from the circtest module for use within the exon module
Assets 2

@tjakobi tjakobi released this Jul 26, 2018 · 163 commits to master since this release

We are proud to release the new version of circtools, 1.1.0.3 as of today.

DOI

Solved issues

  • 1.1.0.3 is a bugfix release that addresses issues when calling the detect and reconstruct module
Assets 2

@tjakobi tjakobi released this Jul 20, 2018 · 172 commits to master since this release

We are proud to release the new version of circtools, 1.1.0.2 as of today.

Solved issues

  • 1.1.0.2 is a bugfix release that fixes an issues in the primer design module yielding to incorrect, non-circRNA specific primer pairs for single-exon circRNAs.
Assets 2
Jul 17, 2018
Version 1.1.0.1 release
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