dieterich-lab/circtools issues and pull requests

#94 - circtools install failes with Python 3.10.6

Issue - State: closed - Opened by HaraldWilhelmi over 2 years ago - 1 comment
Labels: bug

#93 - ValueError: numpy.ndarray size changed, may indicate binary incompatibility.

Issue - State: closed - Opened by HaraldWilhelmi almost 3 years ago - 6 comments

#92 - remapping input should be Unmapped.out.mate or mate of PE?

Issue - State: open - Opened by genebial about 3 years ago

#91 - Fix and clarification for the R dependencies

Pull Request - State: closed - Opened by HaraldWilhelmi over 3 years ago

#90 - Bugfix/docs

Pull Request - State: closed - Opened by HaraldWilhelmi over 3 years ago

#89 - Adding empty requirements.readthedocs.txt for RTD build

Pull Request - State: closed - Opened by tjakobi over 4 years ago

#88 - Preparations for circtools 1.2

Pull Request - State: closed - Opened by tjakobi over 4 years ago

#87 - Sirna

Pull Request - State: closed - Opened by tjakobi about 5 years ago - 1 comment

#86 - Enriched exons

Pull Request - State: closed - Opened by tjakobi over 5 years ago

#85 - circtools exon should support more species

Issue - State: closed - Opened by tjakobi over 5 years ago
Labels: feature, exon

#84 - linear primers in circtools primex for each circRNA candidate

Issue - State: open - Opened by daaaaande over 5 years ago - 1 comment
Labels: enhancement, primer

#83 - primex not intron-aware?

Issue - State: open - Opened by daaaaande over 5 years ago - 3 comments
Labels: bug, primer

#82 - Python2 and 3 support not feasible on HPC environments

Issue - State: open - Opened by Psy-Fer over 5 years ago - 6 comments

#81 - Sirna branch

Pull Request - State: closed - Opened by skambha6 over 5 years ago

#80 - Travis build fails due to statsmodels version bump

Issue - State: closed - Opened by tjakobi over 5 years ago - 1 comment
Labels: bug

#79 - Error in dplyr/rlang version using primex module

Issue - State: closed - Opened by skambha6 over 5 years ago - 1 comment

#78 - circtools installation sets wrong R library folder in .Renviron

Issue - State: closed - Opened by tjakobi over 5 years ago - 1 comment
Labels: bug

#77 - Error installing circtools on Mac OSX due to no wget

Issue - State: closed - Opened by skambha6 over 5 years ago - 1 comment
Labels: bug, enhancement, macos

#76 - Error using R version 3.6

Issue - State: closed - Opened by skambha6 over 5 years ago
Labels: bug, enhancement

#75 - Primex crashes when product length > circRNA length

Issue - State: closed - Opened by tjakobi almost 6 years ago
Labels: bug, primer

#74 - Do reads need to be aligned with "--outSAMattributes NH HI AS nM NM MD jM jI XS" ?

Issue - State: closed - Opened by cmonger almost 6 years ago - 1 comment
Labels: bug, documentation

#73 - circtest PDF labels gone

Issue - State: closed - Opened by tjakobi almost 6 years ago
Labels: bug

#72 - Enrichment Module Errors

Issue - State: closed - Opened by udube about 6 years ago - 9 comments
Labels: bug, enrich

#71 - Primer Design Module Error

Issue - State: closed - Opened by udube about 6 years ago - 4 comments
Labels: bug, primer

#70 - Formatter broken

Issue - State: closed - Opened by tjakobi about 6 years ago
Labels: primer

#69 - Different results for circtest from circtools or from R

Issue - State: open - Opened by idotu about 6 years ago - 2 comments
Labels: bug

#68 - question on grouping for circtest

Issue - State: closed - Opened by idotu about 6 years ago - 1 comment

#67 - The exon module only supports human annotations

Issue - State: closed - Opened by tjakobi over 6 years ago
Labels: enhancement, feature, exon

#66 - Add STAR to required tools

Issue - State: closed - Opened by tjakobi over 6 years ago
Labels: documentation

#65 - Fix broken git ssh clone links

Issue - State: closed - Opened by tjakobi over 6 years ago - 1 comment
Labels: bug, documentation

#64 - Empty lines in the samplesheet file confuse DCC

Issue - State: closed - Opened by tjakobi over 6 years ago
Labels: bug, detect

#63 - Fix -c option for enrich module

Issue - State: closed - Opened by tjakobi over 6 years ago
Labels: bug, enrich

#62 - Provide additional documentation for the enrich module

Issue - State: closed - Opened by tjakobi over 6 years ago
Labels: enhancement, enrich

#61 - Use consistent Python 3 versions in the documentation

Issue - State: closed - Opened by tjakobi over 6 years ago
Labels: documentation

#60 - State clearly that FUCHS and DCC require Python 2

Issue - State: closed - Opened by tjakobi over 6 years ago
Labels: detect, reconstruct, documentation

#59 - Missing python module in install routine

Issue - State: closed - Opened by tjakobi over 6 years ago
Labels: bug, enrich

#58 - Fix broken pysam dependency of HTseq for DCC

Issue - State: closed - Opened by tjakobi over 6 years ago - 1 comment
Labels: bug, detect

#57 - installation error

Issue - State: closed - Opened by circR over 6 years ago - 13 comments
Labels: question

#56 - Integrating changes for successful macOS installation

Pull Request - State: open - Opened by tjakobi over 6 years ago
Labels: enhancement, feature

#55 - Fresh install fails because of statsmodels

Issue - State: closed - Opened by tjakobi over 6 years ago - 2 comments
Labels: bug

#54 - Primex integration

Pull Request - State: closed - Opened by tjakobi almost 7 years ago

#53 - Adding --keep-temp parameter to keep temp files (and re-enabling auto…

Pull Request - State: closed - Opened by tjakobi almost 7 years ago

#52 - Flanking intron integration

Pull Request - State: closed - Opened by tjakobi almost 7 years ago

#51 - New dictionary layout

Pull Request - State: closed - Opened by tjakobi almost 7 years ago

#50 - BED track coordinates are incorrect

Issue - State: closed - Opened by CDieterich about 7 years ago - 1 comment
Labels: bug

#49 - rm biomart - add ensembldb

Pull Request - State: closed - Opened by alexey0308 about 7 years ago

#48 - Add per exon p-value and log2 fold changes to exon Excel output

Issue - State: open - Opened by tjakobi about 7 years ago - 1 comment
Labels: enhancement, reconstruct

#47 - Manual "primer module" missing

Issue - State: closed - Opened by giuseppebenvenuto about 7 years ago - 2 comments
Labels: enhancement, primer

#46 - Unify all enrichment plotting code in one file

Issue - State: closed - Opened by tjakobi about 7 years ago
Labels: enhancement, enrich

#45 - BED file produced by exon usage script misses chromosome column

Issue - State: closed - Opened by tjakobi about 7 years ago
Labels: bug, exon

#44 - Check the processing of single exon genes in terms of circRNA RBP enrichment

Issue - State: closed - Opened by tjakobi over 7 years ago - 1 comment
Labels: question, enrich

#43 - Add a visualization for top enriched circRNAs/RBPs

Issue - State: closed - Opened by tjakobi over 7 years ago - 1 comment
Labels: enhancement, enrich

#42 - Investigate what 'unknown breakpoint' events are

Issue - State: open - Opened by tjakobi over 7 years ago - 1 comment
Labels: question, reconstruct

#41 - Normalize #circRNA isoforms in visualization plots

Issue - State: open - Opened by tjakobi over 7 years ago
Labels: enhancement, enrich

#40 - CircSkipping visualization

Issue - State: closed - Opened by tjakobi over 7 years ago - 1 comment
Labels: enhancement, detect

#39 - Quantile plot for reconstruction module

Issue - State: closed - Opened by tjakobi over 7 years ago
Labels: enhancement, reconstruct

#38 - Include option to generate black and white or grey scale graphs for non-color journals

Issue - State: closed - Opened by tjakobi over 7 years ago
Labels: enhancement, enrich, detect, reconstruct, quickcheck

#37 - R dev

Pull Request - State: closed - Opened by alexey0308 over 7 years ago

#36 - Module to analyse conservation of circRNAs across species

Issue - State: open - Opened by tjakobi over 7 years ago
Labels: feature

#35 - R dev

Pull Request - State: closed - Opened by alexey0308 over 7 years ago

#34 - Correct handling of the number of iterations

Issue - State: closed - Opened by tjakobi over 7 years ago - 2 comments
Labels: bug, enrich

#33 - Length calculation when used in feature mode

Issue - State: closed - Opened by tjakobi over 7 years ago - 1 comment
Labels: bug, enhancement

#32 - X labels of the PDF output are alphabetically ordered

Issue - State: closed - Opened by tjakobi over 7 years ago
Labels: bug, quickcheck

#31 - Add a DCC analysis script able to uncover library problems

Issue - State: closed - Opened by tjakobi over 7 years ago - 1 comment
Labels: enhancement

#30 - Enrichment module produces external bedtools error when using -I *_utr

Issue - State: closed - Opened by tjakobi over 7 years ago - 4 comments
Labels: bug, enrich

#29 - fix #28

Pull Request - State: closed - Opened by alexey0308 over 7 years ago

#28 - primer design R installation script stuck in loop

Issue - State: closed - Opened by tjakobi over 7 years ago - 4 comments
Labels: bug, primer

#27 - Add option to include / exclude specific genomic features during shuffeling

Issue - State: closed - Opened by tjakobi over 7 years ago - 3 comments
Labels: enhancement, feature, enrich

#26 - Visualization option for enrichment module

Issue - State: closed - Opened by tjakobi over 7 years ago - 1 comment
Labels: enhancement, feature

#25 - Provide a sample data set

Issue - State: closed - Opened by tjakobi over 7 years ago - 4 comments
Labels: enhancement

#24 - Module to design siRNAs

Issue - State: open - Opened by tjakobi over 7 years ago - 5 comments
Labels: enhancement, feature

#23 - readme for the package

Pull Request - State: closed - Opened by alexey0308 over 7 years ago

#22 - R dev

Pull Request - State: closed - Opened by alexey0308 over 7 years ago

#21 - Installation instructions for OligoArrayAux software

Issue - State: closed - Opened by tjakobi over 7 years ago - 1 comment
Labels: enhancement

#20 - Installation instructions / link for bedtools

Issue - State: closed - Opened by tjakobi over 7 years ago

#19 - R install script fails on fresh R 3.4.0 install

Issue - State: closed - Opened by tjakobi over 7 years ago - 4 comments
Labels: bug

#18 - r main script ready

Pull Request - State: closed - Opened by alexey0308 over 7 years ago - 2 comments

#17 - error in DECIPHER call to RSQLite

Issue - State: closed - Opened by alexey0308 over 7 years ago - 3 comments
Labels: enhancement

#16 - Remove (py)bedtools dependency

Issue - State: open - Opened by tjakobi over 7 years ago
Labels: enhancement

#15 - Add support for zipped input files

Issue - State: open - Opened by tjakobi over 7 years ago
Labels: enhancement

#14 - Add a possibility to use custom output file names

Issue - State: closed - Opened by tjakobi over 7 years ago

#13 - R dev: add transformation and fix primer design

Pull Request - State: closed - Opened by alexey0308 over 7 years ago

#12 - primer design

Pull Request - State: closed - Opened by alexey0308 almost 8 years ago

#11 - Implement a primer visualization and design wrapper R script

Issue - State: closed - Opened by tjakobi almost 8 years ago - 1 comment
Labels: feature

#10 - How do we optimally integrate DCC and FUCHS?

Issue - State: closed - Opened by tjakobi almost 8 years ago - 1 comment
Labels: enhancement

#9 - Integration of FUCHS

Issue - State: closed - Opened by tjakobi almost 8 years ago - 1 comment
Labels: feature

#8 - Integration of DCC

Issue - State: closed - Opened by tjakobi almost 8 years ago - 1 comment
Labels: feature

#7 - Add framework for R installation to setup script

Issue - State: closed - Opened by tjakobi almost 8 years ago - 2 comments
Labels: feature

#6 - Integration of the alternative exon usage script

Issue - State: closed - Opened by tjakobi almost 8 years ago - 3 comments
Labels: feature

#5 - Integration of CircTest

Issue - State: closed - Opened by tjakobi almost 8 years ago - 2 comments
Labels: feature

#4 - Establish a stable version of the circtools platform

Issue - State: closed - Opened by tjakobi almost 8 years ago - 1 comment
Labels: feature

#3 - Adding unit tests to existing code base

Issue - State: open - Opened by tjakobi almost 8 years ago
Labels: enhancement, feature

#2 - Finish implementation of permutation testing

Issue - State: closed - Opened by tjakobi almost 8 years ago
Labels: feature

#1 - package documentation

Pull Request - State: closed - Opened by alexey0308 almost 8 years ago - 1 comment

GitHub / dieterich-lab/circtools issues and pull requests