CHANGELOG.md

In BIMSBbioinfo/ciRcus: Annotation, analysis and visualization of circRNA data

ciRcus 0.1.7

IMPROVEMENTS AND BUG FIXES

• 18-column find_circ output (wherever it comes from) supported

ciRcus 0.1.6

NEW FEATURES

• new bedTracks()/writeBedTracks() functions generating BED6-style GRangesList/writing BED files for circRNA browser tracks
• added D. melanogaster (dm6) and R. norvegicus (rn6) support

IMPROVEMENTS AND BUG FIXES

• using "coarse" pruning.mode in keepStandardChromosomes when building annotation
• introduced a number of bugfixes (and probably new bugs)

ciRcus 0.1.5

NEW FEATURES

• loadAnnotation() converted to S4, can digest both TxDb objects and their sqlite dumps

IMPROVEMENTS AND BUG FIXES

• circLinRatio bug that prevented the ratio from being calculated in 0.1.4 fixed
• many under-the-hood improvements (travis, lintr, codecov...) users will indirectly benefit from

ciRcus 0.1.4

NEW FEATURES

• CIRI2 support
• WBcel235 genome assembly supported
• QC plot for total vs. unique reads

IMPROVEMENTS AND BUG FIXES

• sample order from colData is not broken by summarizeCircs
• system.file call fixed in README

ciRcus 0.1.3

NEW FEATURES

• find_circ2 supported

IMPROVEMENTS AND BUG FIXES

• different coordinate indexing in input and annotation will be automatically detected and fixed
• lots of under-the-hood improvements

ciRcus 0.1.2

NEW FEATURES

• find_circ.py v1.2 supported

ciRcus 0.1.1

NEW FEATURES

• input is loaded into a SummarizedExperiment object
• basic circBase interaction

IMPROVEMENTS AND BUG FIXES

• unit tests

BIMSBbioinfo/ciRcus documentation built on May 5, 2019, 10:25 a.m.