YeoLab/clipper issues and pull requests

#117 - Clipper does not output anything

Issue - State: open - Opened by ramirobarrantes about 1 month ago

#116 - invalid contig chr3

Issue - State: open - Opened by tslzs 12 months ago

#115 - reverse_strand argument for seCLIP peaks?

Issue - State: open - Opened by arun-krishnaraj over 1 year ago

#114 - Move `data` outside of CLIPper such that users can easily make different reference w/o re-installing

Pull Request - State: closed - Opened by algaebrown over 1 year ago - 4 comments

#113 - Problem using Clipper with a cytoplasmic RBP that binds to spliced mRNA

Issue - State: open - Opened by Braulium over 1 year ago

#112 - Exception errors when running pool.py (list index out of range)(SOVLED)

Issue - State: closed - Opened by zhaoshuoxp over 1 year ago - 1 comment

#111 - How to know the peaks called after clipper

Issue - State: open - Opened by ELMMA-FUNNY almost 2 years ago - 3 comments

#110 - why poisson_cutoff not actually used in call_peak.py since it is an additional significance filtering based on count

Issue - State: open - Opened by HUNNNGRY almost 2 years ago

#109 - A solution to core dumped and/or running too slow

Issue - State: open - Opened by YichaoOU almost 2 years ago - 2 comments

#108 - fix index out of range

Pull Request - State: closed - Opened by kstangline about 2 years ago

#107 - Runtime of CLIPer?

Issue - State: open - Opened by mhorlacher about 2 years ago - 3 comments

#106 - CLIPper runs forever for empty bam files

Issue - State: open - Opened by algaebrown about 2 years ago

#105 - CLIPper complains file does not exist while it obviously exists

Issue - State: open - Opened by algaebrown about 2 years ago - 2 comments

#104 - Update peaksmodule.cc

Pull Request - State: open - Opened by y9c over 2 years ago

#103 - clipper displays unusual help messages and can't be used

Issue - State: open - Opened by kerenzhou062 over 2 years ago - 9 comments

#102 - pre-mRNA option not working?

Issue - State: closed - Opened by jmcalabr over 2 years ago - 1 comment

#101 - Main.py fails to import call_peaks.py, prints usage for peaksmodule.cc instead

Issue - State: open - Opened by lee-van over 2 years ago - 2 comments

#100 - Remove PCR duplicates using barcode_collapse_pe.py or picard?

Issue - State: closed - Opened by amdreamer over 2 years ago - 1 comment

#99 - clipperhelper

Issue - State: closed - Opened by kopardev almost 3 years ago - 1 comment

#98 - Multiple fragmented peaks where single peak expected

Issue - State: open - Opened by omarwagih almost 3 years ago

#97 - error with clipper and scipy version

Issue - State: open - Opened by byee4 about 3 years ago

#96 - Issue processing bam file (index out of error)

Issue - State: closed - Opened by omarwagih about 3 years ago - 6 comments

#95 - error on main.py

Issue - State: closed - Opened by alexmondaini about 3 years ago - 2 comments

#94 - Run test ERROR: python -m unittest discover ; The following error is reported. Can the clipper still be used normally

Issue - State: open - Opened by geng-lee over 3 years ago - 3 comments

#93 - Invalid contig error

Issue - State: open - Opened by jalalsiddiqui over 3 years ago - 9 comments

#92 - pip install clipper --user

Issue - State: open - Opened by jalalsiddiqui over 3 years ago - 2 comments

#91 - Having trouble installing clipper

Issue - State: open - Opened by jalalsiddiqui over 3 years ago - 2 comments

#90 - Clipper installation fails

Issue - State: open - Opened by ekfiagbedzi over 3 years ago - 3 comments

#89 - Install Clipper via Conda

Issue - State: open - Opened by gpratt over 3 years ago - 1 comment

#88 - 'Segmentation fault' issue

Issue - State: open - Opened by dahun73 over 3 years ago - 13 comments

#87 - Clipper doesn't recognize contigs from GRCh38, even with GRCh38 given as species

Issue - State: closed - Opened by MattBrauer almost 4 years ago - 11 comments

#86 - `clipper -h` fails after clean install

Issue - State: open - Opened by MattBrauer almost 4 years ago - 6 comments

#85 - Save pickle don’t work

Issue - State: closed - Opened by algaebrown almost 4 years ago

#84 - clipper -h with differerent help documentation

Issue - State: closed - Opened by junjunlab almost 4 years ago - 1 comment

#83 - clipper -h

Issue - State: open - Opened by junjunlab almost 4 years ago - 2 comments

#82 - CLIPper doesn't work with a different help document.

Issue - State: open - Opened by IrisWEI-1996 almost 4 years ago - 11 comments

#81 - rmdup software

Issue - State: closed - Opened by yx-xu almost 4 years ago - 3 comments

#80 - Charlene py3

Pull Request - State: closed - Opened by algaebrown almost 4 years ago

#79 - invalid contig error when running clipper on dm3

Issue - State: open - Opened by jkkbuddika almost 4 years ago - 1 comment

#78 - License to integrate it into conda and galaxy

Issue - State: closed - Opened by heylf about 4 years ago - 1 comment

#77 - About "--bonferroni -- superlocal"

Issue - State: closed - Opened by Li-Yupeng over 4 years ago - 1 comment
Labels: options

#76 - chrM error

Issue - State: open - Opened by tianxiahuihui over 4 years ago - 5 comments
Labels: enhancement

#75 - clipper installation error

Issue - State: closed - Opened by zhenzhenyang-psu over 4 years ago - 2 comments
Labels: upgrade

#74 - Clipper with non model organisms

Issue - State: open - Opened by matthew-valentine over 4 years ago - 3 comments
Labels: options

#73 - ValueError: hg19.AS.STRUCTURE.COMPILED.gff.AS.STRUCTURE.COMPILED.gff does not exist

Issue - State: closed - Opened by maheshmathe almost 5 years ago

#72 - ERROR:root:failed to build spline

Issue - State: closed - Opened by b3b3gg almost 5 years ago - 5 comments
Labels: bug

#71 - install failed

Issue - State: closed - Opened by lll16 almost 5 years ago - 3 comments

#70 - Value error: invalid contig

Issue - State: closed - Opened by njaberi almost 5 years ago

#69 - clipper -h failed

Issue - State: closed - Opened by lmanchon about 5 years ago - 5 comments
Labels: upgrade

#68 - how to configure genome annotation from custom gtf such as mm10 of encode?

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

#67 - a bug for 'clipper/src/readsToWiggle.pyx' in line 79 of version 1.2.1

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

#66 - CLIPper runs and runs

Issue - State: open - Opened by ledwmp over 5 years ago - 4 comments
Labels: question

#65 - Python 3 support

Issue - State: closed - Opened by rekado over 5 years ago - 5 comments
Labels: upgrade

#64 - Running clipper on Encode data: ERROR:root:peak finding failed

Issue - State: closed - Opened by tefina almost 7 years ago - 6 comments
Labels: upgrade