Releases: dieterich-lab/circtools
circtools 1.1.0.2 released
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.
circtools 1.1.0 released
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 [email protected].
We appreciate your feedback and will do what we can to assist you in using circtools.
First version of circtools released [1.0.0]
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.