Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
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
#48 - `MergeMotifsAcrossRuns.ipynb` should account for indexes with respect to `--window`
Issue -
State: open - Opened by KnightAsterial 9 months ago
#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
#44 - `modisco meme` command does not return trimmed motifs and no negative patterns but only positive ones
Issue -
State: open - Opened by ThorbenMaa about 1 year ago
- 3 comments
#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
#38 - Need to raise an error if the attr or ohe files don't end in `.npz` or `.npy`
Issue -
State: open - Opened by jmschrei about 1 year ago
#37 - Errors from MEME text parser leads to pandas.errors.EmptyDataError: No columns to parse from file
Issue -
State: open - Opened by anupamajha1 about 1 year ago
- 2 comments
#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