@tjakobi tjakobi released this Oct 1, 2018

Assets 2

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)

@tjakobi tjakobi released this Aug 3, 2018 · 48 commits to master since this release

Assets 2

Solved issues

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

@tjakobi tjakobi released this Aug 3, 2018 · 50 commits to master since this release

Assets 2

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

@tjakobi tjakobi released this Aug 3, 2018 · 53 commits to master since this release

Assets 2

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
Pre-release

@tjakobi tjakobi released this Aug 3, 2018 · 50 commits to master since this release

Assets 2

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

@tjakobi tjakobi released this Jul 26, 2018 · 56 commits to master since this release

Assets 2

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

@tjakobi tjakobi released this Jul 20, 2018 · 65 commits to master since this release

Assets 2

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.
Jul 17, 2018
Version 1.1.0.1 release

@tjakobi tjakobi released this Jul 17, 2018 · 69 commits to master since this release

Assets 2

We are proud to release the new version of circtools, 1.1.0 as of today.

New modules in version 1.1.0:

quickcheck

A quality check of the employed libraries after read mapping and detection of circRNAs.

circtest

Statistical testing, e.g. host gene-independent expression and RNase R enrichment

exon

Detect RNase R-resistant exons within circRNAs

primer

The primer command is used to design and visualize primers required for follow up wet lab experiments to verify circRNA candidates. The backend was changed to use the in-house primex library by @alexey0308.

Updated modules in version 1.1.0:

detect

The detect command is an interface to DCC, also developed at the Dieterich lab. DCC is a circular RNA detection tool based on STAR alignment files.

reconstruct

The reconstruct command is an interface to FUCHS. The module (https://github.com/dieterich-lab/FUCHS) is employing DCC-generated data to reconstruct circRNA structures.

enrich

The enrichment module may be used to identify circRNAs enriched for specific RNA binding proteins (RBP) based on DCC-identified circRNAs and processed eCLIP data. For K526 and HepG2 cell lines plenty of this data is available through the ENCODE project.

Solved issues

21 Issues could be closed/fixed:

  • #55 Fresh install fails because of statsmodels bug
  • #50 BED track coordinates are incorrect bug
  • #47 Manual "primer module" missing enhancement primer
  • #46 Unify all enrichment plotting code in one file enhancement enrich
  • #45 BED file produced by exon usage script misses chromosome column bug exon
  • #44 Check the processing of single exon genes in terms of circRNA RBP enrichment
  • #43 Add a visualization for top enriched circRNAs/RBPs enhancement enrich
  • #40 CircSkipping visualization detect enhancement
  • #39 Quantile plot for reconstruction module enhancement reconstruct
  • #38 Include option to generate black and white or grey scale graphs for non-color journals
  • #34 Correct handling of the number of iterations bug enrich
  • #33 Length calculation when used in feature mode bug enhancement
  • #32 X labels of the PDF output are alphabetically ordered bug quickcheck
  • #31 Add a DCC analysis script able to uncover library problems enhancement
  • #30 Enrichment module produces external bedtools error when using -I *_utr bug
  • #28 primer design R installation script stuck in loop bug primer
  • #27 Add option to include / exclude specific genomic features during shuffeling
  • #26 Visualization option for enrichment module enhancement feature
  • #17 error in DECIPHER call to RSQLite enhancement
  • #6 Integration of the alternative exon usage script feature
  • #5 Integration of CircTest feature

Having issues?

Please be so kind and send us a message via the issue form or directly to circtools@dieterichlab.org.

We appreciate your feedback and will do what we can to assist you in using circtools.

Assets 2

We are proud to release the first version of circtools, version 1.0.0 as of today.

The 0.1 branch contains the following modules:

detect

The detect command is an interface to DCC, also developed at the Dieterich lab. DCC is a circular RNA detection tool based on STAR alignment files.

reconstruct

The reconstruct command is an interface to FUCHS. FUCHS is employing DCC-generated data to reconstruct circRNA structures.

primer

The primer command is used to design and visualize primers required for follow up wet lab experiments to verify circRNA candidates.

enrich

The enrichment module may be used to identify circRNAs enriched for specific RNA binding proteins (RBP) based on DCC-identified circRNAs and processed eCLIP data. For K526 and HepG2 cell lines plenty of this data is available through the ENCODE project.

Having issues?

Please be so kind and top us a message via the issue form. We appreciate your feedback and will do what we can to assist you in using circtools.