Ecosyste.ms: Issues

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GitHub / saketkc/riboraptor issues and pull requests

#34 - riboraptor version: 0.2.2-0.4.0 no configs file found

Issue - State: closed - Opened by cnrs about 5 years ago - 1 comment

#33 - Added new Snakefile for processing starting from bams and a wrapper f…

Pull Request - State: closed - Opened by saketkc about 6 years ago - 1 comment

#31 - Add coherence score

Pull Request - State: closed - Opened by saketkc about 6 years ago

#30 - Added shiftbw method to shift a bigwig by a certain number of bases

Pull Request - State: closed - Opened by saketkc about 6 years ago

#29 - Added notebook describing possible queries for SRA metadata

Pull Request - State: closed - Opened by saketkc about 6 years ago - 1 comment

#27 - Add a method to find overrepresented kmers

Pull Request - State: closed - Opened by saketkc about 6 years ago - 2 comments

#26 - adaptor trimming

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

#24 - Periodicity plotter

Pull Request - State: closed - Opened by saketkc about 6 years ago

#23 - snakemake progress out of sync

Issue - State: closed - Opened by saketkc about 6 years ago
Labels: wontfix

#22 - Erroneous trimming

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

#21 - Add a method to calculate distance between profiles

Issue - State: closed - Opened by saketkc about 6 years ago - 1 comment
Labels: enhancement

#20 - BAM summarizer, multi fragment bigwig support

Pull Request - State: closed - Opened by saketkc about 6 years ago - 2 comments
Labels: bug, enhancement

#19 - Added functionality to summarize everything in one file

Pull Request - State: closed - Opened by saketkc over 6 years ago

#18 - convert all 1-based intervals to 0-based

Issue - State: closed - Opened by wenzhenl over 6 years ago

#17 - riboraptor infer-protocol gives different results on Ribo-seq data of rps5

Issue - State: closed - Opened by wenzhenl over 6 years ago - 8 comments

#16 - removed creating index step

Pull Request - State: closed - Opened by wenzhenl over 6 years ago - 3 comments

#15 - infer-protocol fails on transcriptome-based bams

Issue - State: closed - Opened by wenzhenl over 6 years ago - 6 comments

#14 - Add bam-coverage, lengthwise strand aware tracking.

Pull Request - State: closed - Opened by saketkc over 6 years ago - 6 comments

#13 - Remove TODO.md and use issue instead?

Issue - State: closed - Opened by wenzhenl over 6 years ago - 2 comments

#12 - Periodicity for each coverage

Issue - State: closed - Opened by wenzhenl over 6 years ago
Labels: TODO

#11 - Fix strand-aware counting and p-site correction based on reads' length

Issue - State: closed - Opened by wenzhenl over 6 years ago - 1 comment
Labels: TODO

#10 - updated TODO

Pull Request - State: closed - Opened by wenzhenl over 6 years ago - 2 comments

#9 - Infer protocol

Pull Request - State: closed - Opened by saketkc over 6 years ago - 2 comments

#8 - is riboraptor download-sra working?

Issue - State: closed - Opened by wenzhenl over 6 years ago

#7 - is ignore_tx_version needed?

Issue - State: closed - Opened by wenzhenl over 6 years ago - 13 comments

#6 - Reformatted version

Pull Request - State: closed - Opened by saketkc over 6 years ago - 11 comments

#5 - refactored and optimized count related functions

Pull Request - State: closed - Opened by wenzhenl over 6 years ago - 8 comments

#4 - Update example_workflow.rst

Pull Request - State: closed - Opened by HodaMirsafian over 6 years ago

#3 - new command: uniq-bam

Pull Request - State: closed - Opened by saketkc over 6 years ago

#2 - Some typo errors in html manual

Issue - State: closed - Opened by HodaMirsafian almost 7 years ago - 1 comment

#1 - copyright statement

Issue - State: closed - Opened by xjlizji almost 7 years ago