Ecosyste.ms: Issues

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GitHub / jmschrei/tfmodisco-lite issues and pull requests

#55 - Fix bug in gapped kmer

Pull Request - State: open - Opened by thomasopsomer about 2 months ago - 4 comments

#54 - Generate basic report with out meme comparison

Issue - State: open - Opened by kaillahs 4 months ago - 13 comments

#53 - necessity for the calling of use("pdf")

Issue - State: open - Opened by ruochiz 4 months ago - 5 comments

#52 - problem in tfmodisco input

Issue - State: closed - Opened by GGboy-Zzz 5 months ago - 3 comments

#51 - Compatibility with bpnet-refactor

Issue - State: closed - Opened by gregorydonahue 6 months ago - 2 comments

#50 - Trouble constructing minimal example where motifs are found

Issue - State: closed - Opened by nickackerman42 7 months ago - 4 comments

#49 - Prediction from low peak quality (qval)

Issue - State: open - Opened by arodel21 8 months ago - 2 comments

#47 - How are high absolute attribution scores defined?

Issue - State: open - Opened by FelixWaern 9 months ago - 1 comment

#46 - works with variable length sequences

Pull Request - State: open - Opened by akmorrow13 10 months ago

#45 - --verbose is still rather taciturn

Issue - State: open - Opened by mmtrebuchet 10 months ago - 1 comment

#43 - Center peak regions at summit in `modisco seqlet-bed`

Issue - State: open - Opened by austintwang about 1 year ago - 1 comment

#42 - Fix `modisco convert`

Pull Request - State: closed - Opened by austintwang about 1 year ago - 1 comment

#41 - Support seqlet position data in `modisco convert`

Pull Request - State: closed - Opened by austintwang about 1 year ago - 2 comments

#40 - Print useful error message when `tomtom` is missing

Pull Request - State: closed - Opened by ivyraine about 1 year ago

#39 - `example_idx` doesnt trace back to original contribution scores

Issue - State: open - Opened by mlweilert about 1 year ago - 1 comment

#36 - Display defaults in help output

Pull Request - State: closed - Opened by austintwang over 1 year ago

#35 - build: Remove upper bound on requires-python

Pull Request - State: closed - Opened by matthewfeickert over 1 year ago - 2 comments

#34 - Add Unit tests

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

#33 - Add TOMTOM matrix file-writing, and add report `-t` flag for it

Pull Request - State: closed - Opened by ivyraine over 1 year ago

#32 - Updated report.py to save tomtom output at tomtom.tsv

Pull Request - State: closed - Opened by soumyakundu over 1 year ago - 1 comment

#31 - Add negative strand patterns to `meme` output

Pull Request - State: closed - Opened by ivyraine over 1 year ago

#30 - Add negative pattern implementation for `meme` subcommand

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

#29 - Add BED and FASTA output subcommands `seqlet-bed` and `seqlet-fasta`

Pull Request - State: closed - Opened by ivyraine over 1 year ago - 1 comment

#28 - Add example notebooks

Pull Request - State: closed - Opened by ivyraine over 1 year ago

#27 - (WIP) Implement MEME output subcommand `meme`

Pull Request - State: closed - Opened by ivyraine over 1 year ago - 5 comments

#26 - motifs.html report can be confusing

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

#25 - version for RNA sequence

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

#24 - Add command to extract seqlets info in BED and FASTA format

Issue - State: closed - Opened by jmschrei over 1 year ago

#23 - Add MEME output from modisco motifs

Issue - State: closed - Opened by jmschrei over 1 year ago

#22 - Add example folder containing notebooks

Issue - State: closed - Opened by jmschrei over 1 year ago

#21 - Access motifs

Issue - State: open - Opened by samuel-g-bates over 1 year ago

#20 - Reset seqlet coordinates with respect to "--window"

Issue - State: open - Opened by jvierstra over 1 year ago - 1 comment

#19 - Add Linting Github Action

Issue - State: open - Opened by ivyraine over 1 year ago - 1 comment

#18 - (READY) Make motif database-based reporting optional

Pull Request - State: closed - Opened by ivyraine over 1 year ago - 2 comments

#17 - Update Python version req to include 3.10.x

Pull Request - State: closed - Opened by ivyraine over 1 year ago

#16 - Update README to include TOMTOM requirement

Pull Request - State: closed - Opened by ivyraine over 1 year ago - 2 comments

#15 - Specify Python version requirement

Pull Request - State: closed - Opened by ivyraine over 1 year ago

#14 - Doesn't work for the the sequences in variable lengths

Issue - State: closed - Opened by ruizhideng over 1 year ago - 2 comments

#13 - Running tfmodisco-lite for multiple tasks?

Issue - State: closed - Opened by ioansarr over 1 year ago - 4 comments

#12 - Could not construct partition: Cannot accept NaN weights.

Issue - State: open - Opened by avantikalal over 1 year ago - 1 comment

#11 - Motifs missing when input sequence less than 400 bp

Issue - State: closed - Opened by ziwei-75 over 1 year ago - 1 comment

#10 - Does tfmodisco-lite work with sequences that contain N?

Issue - State: closed - Opened by coffeebond almost 2 years ago - 2 comments

#9 - tabs vs spaces

Issue - State: closed - Opened by hopdebee almost 2 years ago - 1 comment

#8 - No motifs found

Issue - State: open - Opened by SalimMegat almost 2 years ago - 1 comment

#7 - Request of the example data

Issue - State: closed - Opened by Gavin-Lijy almost 2 years ago - 3 comments

#6 - function, CLI cmd to convert backward to old modisco results file format

Pull Request - State: closed - Opened by kellycochran almost 2 years ago

#5 - Create reports without meme database

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

#4 - Arial Rounded not available on my system

Issue - State: closed - Opened by mmtrebuchet about 2 years ago - 1 comment

#3 - Matrix format of pfms in motif pfms directory

Issue - State: closed - Opened by due23 about 2 years ago - 3 comments

#2 - Generating report: pandas.errors.EmptyDataError: No columns to parse from file

Issue - State: closed - Opened by due23 about 2 years ago - 1 comment

#1 - Attribution scores vs importance scores

Issue - State: closed - Opened by due23 about 2 years ago - 2 comments