jmschrei tfmodisco-lite issues

jmschrei / tfmodisco-lite

A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.

MIT License

56 stars 16 forks source link

issues

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Fix bug in gapped kmer

#55 thomasopsomer opened 5 days ago
4
Generate basic report with out meme comparison

#54 kaillahs opened 2 months ago
13
necessity for the calling of use("pdf")

#53 ruochiz opened 2 months ago
5
problem in tfmodisco input

#52 GGboy-Zzz closed 3 months ago
3
Compatibility with bpnet-refactor

#51 gregorydonahue closed 4 months ago
2
Trouble constructing minimal example where motifs are found

#50 nickackerman42 closed 5 months ago
4
Prediction from low peak quality (qval)

#49 arodel21 opened 6 months ago
2
`MergeMotifsAcrossRuns.ipynb` should account for indexes with respect to `--window`

#48 KnightAsterial opened 7 months ago
0
How are high absolute attribution scores defined?

#47 FelixWaern opened 8 months ago
1
works with variable length sequences

#46 akmorrow13 opened 8 months ago
0
--verbose is still rather taciturn

#45 mmtrebuchet opened 8 months ago
1
`modisco meme` command does not return trimmed motifs and no negative patterns but only positive ones

#44 ThorbenMaa opened 11 months ago
3
Center peak regions at summit in `modisco seqlet-bed`

#43 austintwang opened 1 year ago
1
Fix `modisco convert`

#42 austintwang closed 1 year ago
1
Support seqlet position data in `modisco convert`

#41 austintwang closed 1 year ago
2
Print useful error message when `tomtom` is missing

#40 bytewife closed 1 year ago
0
`example_idx` doesnt trace back to original contribution scores

#39 mlweilert opened 1 year ago
1
Need to raise an error if the attr or ohe files don't end in `.npz` or `.npy`

#38 jmschrei opened 1 year ago
0
Errors from MEME text parser leads to pandas.errors.EmptyDataError: No columns to parse from file

#37 anupamajha1 opened 1 year ago
2
Display defaults in help output

#36 austintwang closed 1 year ago
0
build: Remove upper bound on requires-python

#35 matthewfeickert closed 1 year ago
2
Add Unit tests

#34 bytewife opened 1 year ago
0
Add TOMTOM matrix file-writing, and add report `-t` flag for it

#33 bytewife closed 1 year ago
0
Updated report.py to save tomtom output at tomtom.tsv

#32 soumyakundu closed 1 year ago
1
Add negative strand patterns to `meme` output

#31 bytewife closed 1 year ago
0
Add negative pattern implementation for `meme` subcommand

#30 bytewife opened 1 year ago
0
Add BED and FASTA output subcommands `seqlet-bed` and `seqlet-fasta`

#29 bytewife closed 1 year ago
1
Add example notebooks

#28 bytewife closed 1 year ago
0
(WIP) Implement MEME output subcommand `meme`

#27 bytewife closed 1 year ago
5
motifs.html report can be confusing

#26 janewangsmile opened 1 year ago
0
version for RNA sequence

#25 janewangsmile opened 1 year ago
0
Add command to extract seqlets info in BED and FASTA format

#24 jmschrei closed 1 year ago
0
Add MEME output from modisco motifs

#23 jmschrei closed 1 year ago
0
Add example folder containing notebooks

#22 jmschrei closed 1 year ago
0
Access motifs

#21 samuel-g-bates opened 1 year ago
0
Reset seqlet coordinates with respect to "--window"

#20 jvierstra opened 1 year ago
1
Add Linting Github Action

#19 bytewife opened 1 year ago
1
(READY) Make motif database-based reporting optional

#18 bytewife closed 1 year ago
2
Update Python version req to include 3.10.x

#17 bytewife closed 1 year ago
0
Update README to include TOMTOM requirement

#16 bytewife closed 1 year ago
2
Specify Python version requirement

#15 bytewife closed 1 year ago
0
Doesn't work for the the sequences in variable lengths

#14 ruizhideng closed 1 year ago
2
Running tfmodisco-lite for multiple tasks?

#13 ioansarr closed 1 year ago
4
Could not construct partition: Cannot accept NaN weights.

#12 avantikalal opened 1 year ago
1
Motifs missing when input sequence less than 400 bp

#11 ziwei-75 closed 1 year ago
1
Does tfmodisco-lite work with sequences that contain N?

#10 coffeebond closed 1 year ago
2
tabs vs spaces

#9 hopdebee closed 1 year ago
1
No motifs found

#8 SalimMegat opened 1 year ago
1
Request of the example data

#7 Gavin-Lijy closed 1 year ago
3
function, CLI cmd to convert backward to old modisco results file format

#6 kellycochran closed 1 year ago
0