Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / kundajelab/tfmodisco issues and pull requests

#118 - Memory for more than 50 sequences with length of 250K

Issue - State: open - Opened by Yaoyx 4 months ago

#117 - AssertionError when run tf-modisco

Issue - State: open - Opened by Jie-Lii 4 months ago - 1 comment

#116 - Average Contribution Score

Issue - State: open - Opened by shunyasanuma 4 months ago - 1 comment

#115 - ValueError: cannot reshape array of size 0 into shape (0,newaxis)

Issue - State: open - Opened by Yaoyx 8 months ago - 1 comment

#114 - Non-zeros in pattern["task0_contrib_scores"]["fwd"]

Issue - State: closed - Opened by Yaoyx 8 months ago - 1 comment

#113 - Mean-normalize hypothetical contributions

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

#112 - ValueError: perplexity must be less than n_samples

Issue - State: closed - Opened by velten-lab 10 months ago - 5 comments

#110 - relating patternidx from hit scoring to identified motifs

Issue - State: closed - Opened by camiel-m over 1 year ago

#109 - Confusion with negative motifs

Issue - State: open - Opened by PelFritz over 1 year ago - 4 comments

#108 - fix tsne sparse input matrix error

Pull Request - State: closed - Opened by akmorrow13 over 1 year ago - 5 comments

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

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

#106 - Adding padding during sequel detection results in invalid coordinates

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

#104 - Which settings of modisco should I change

Issue - State: open - Opened by PelFritz over 2 years ago

#103 - Comparing motifs from TFMoDisco and other methods?

Issue - State: open - Opened by sandraleebatista over 2 years ago - 1 comment

#102 - TypeError: '<=' not supported between instances of 'list' and 'float'

Issue - State: open - Opened by mhorlacher over 2 years ago - 4 comments

#101 - Bugfix in coordproducers.py for python 3.9.7

Pull Request - State: open - Opened by MartGro over 2 years ago - 4 comments

#100 - How to extract seqlets

Issue - State: closed - Opened by PelFritz over 2 years ago - 10 comments

#99 - Trying to bring down Leiden memory use - 1

Pull Request - State: closed - Opened by AvantiShri almost 3 years ago

#98 - Adding Circleci continuous integration

Pull Request - State: closed - Opened by AvantiShri almost 3 years ago

#96 - TfModiscoWorkflow breaks at coo_mat

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

#94 - Improvements to hit scoring

Pull Request - State: closed - Opened by AvantiShri over 3 years ago

#93 - Added back in functionality for "final_flank_to_add" (0.5.14.2)

Pull Request - State: closed - Opened by AvantiShri over 3 years ago

#92 - ENH: gitignore and remove modisco.egg-info

Pull Request - State: closed - Opened by kaczmarj over 3 years ago - 1 comment

#91 - v0.5.14.1 Nicer API for the density-adaptive hit scoring

Pull Request - State: closed - Opened by AvantiShri over 3 years ago

#89 - AssertionError : assert len(new_pattern)==1 in modisco/aggregator.py

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

#87 - Fixed n_jobs bug that arose with old gapped kmer embdder

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

#85 - Parallelizing Leiden

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

#83 - Sparse Matrices Memory Reduction

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

#82 - Reverting default setting, minor fixes

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

#81 - Bug in checking weights sum to 1

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

#80 - Changing sum-to-1 error to a warning for calculating information content

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

#79 - AssertionError: Probabilities don't sum to 1

Issue - State: closed - Opened by BeyondTheProof almost 4 years ago - 10 comments

#78 - Lower Mem AGKM + Variable Len Seqlet ID + Exemplar-Based Hit Scoring

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

#77 - Potential fix for division-by-zero error

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

#76 - Small fixes

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

#75 - AssertionError: Probabilities don't sum to 1 along axis 1

Issue - State: closed - Opened by Shunili almost 4 years ago - 2 comments

#73 - Developing a different strategy for merging clusters

Pull Request - State: closed - Opened by AvantiShri about 4 years ago

#72 - Implemented saving and loading of pattern merge hierarchy

Pull Request - State: closed - Opened by AvantiShri about 4 years ago

#70 - Retrying what was supposed to be PR 67

Pull Request - State: closed - Opened by AvantiShri about 4 years ago

#69 - Revert "Trying Cython"

Pull Request - State: closed - Opened by AvantiShri about 4 years ago

#68 - Revert "Few fixes and additional features"

Pull Request - State: closed - Opened by AvantiShri about 4 years ago

#67 - Few fixes and additional features

Pull Request - State: closed - Opened by AvantiShri about 4 years ago

#64 - Trying Cython

Pull Request - State: closed - Opened by AvantiShri about 4 years ago

#63 - Advanced gapped kmer, IC-based motif centering

Pull Request - State: closed - Opened by AvantiShri over 4 years ago

#62 - Pushing the interactive plots feature to master

Pull Request - State: closed - Opened by AvantiShri over 4 years ago

#60 - revcomp flag, singleton init in addition to cluster init for Leiden

Pull Request - State: closed - Opened by AvantiShri over 4 years ago

#59 - Dependency fix for leidenalg and tqdm

Pull Request - State: closed - Opened by AvantiShri over 4 years ago

#58 - libary import leidenalg and tqdm is missing in the dependencies

Issue - State: closed - Opened by visze over 4 years ago - 1 comment

#57 - Support for MEME-based initialization

Pull Request - State: closed - Opened by AvantiShri over 4 years ago

#56 - Ability to specify a plot save directory

Pull Request - State: closed - Opened by AvantiShri over 4 years ago

#55 - Scikit version compatibility fix

Pull Request - State: closed - Opened by AvantiShri almost 5 years ago

#54 - Increase offset for weakest_transformed_thresh

Pull Request - State: closed - Opened by mmtrebuchet almost 5 years ago - 1 comment

#53 - Increase probability sum tolerance

Pull Request - State: closed - Opened by mmtrebuchet almost 5 years ago - 1 comment

#52 - Replaced dense affinity matrix with sparse ones

Pull Request - State: closed - Opened by AvantiShri almost 5 years ago

#51 - Added functionality for just extracting seqlets

Pull Request - State: closed - Opened by AvantiShri almost 5 years ago

#50 - avoid memory bottleneck

Pull Request - State: closed - Opened by hy395 about 5 years ago - 1 comment

#49 - memory usage bottleneck

Issue - State: open - Opened by hy395 about 5 years ago - 4 comments

#48 - Syncing latest changes with branch where I am doing the refactoring

Pull Request - State: closed - Opened by AvantiShri about 5 years ago

#47 - Bugfix to avoid nan values in modisco.affinitymat.NumpyCosineSimilarity

Pull Request - State: closed - Opened by AvantiShri about 5 years ago

#46 - Updated hit scoring

Pull Request - State: closed - Opened by AvantiShri about 5 years ago

#45 - Reduced memory usage

Pull Request - State: closed - Opened by AvantiShri over 5 years ago

#44 - Initial version of clustering that uses the conv filter activations

Pull Request - State: open - Opened by AvantiShri over 5 years ago - 1 comment

#43 - Fixing potential div by 0 error

Pull Request - State: closed - Opened by AvantiShri over 5 years ago

#42 - Update metaclusterers.py

Pull Request - State: open - Opened by AvantiShri over 5 years ago - 1 comment

#41 - viz_sequence plot

Issue - State: closed - Opened by MMostavi over 5 years ago - 2 comments

#40 - prevent negative values from being passed to pairwise distances

Pull Request - State: closed - Opened by rosaxma over 5 years ago

#39 - Added support for different manual positive and negative thresholds

Pull Request - State: closed - Opened by AvantiShri over 5 years ago

#38 - Added support for NOT using reverse complements when computing the similarity matrix

Pull Request - State: closed - Opened by AvantiShri over 5 years ago - 1 comment

#37 - Added `min_metacluster_size_frac`

Pull Request - State: closed - Opened by Avsecz almost 6 years ago - 3 comments

#36 - Improved Null Distributions

Pull Request - State: closed - Opened by AvantiShri almost 6 years ago

#35 - Create LICENSE

Pull Request - State: closed - Opened by AvantiShri almost 6 years ago

#34 - value provider task_name fixed

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

#33 - NaN or High value for dtype float32

Issue - State: open - Opened by TommyJW about 6 years ago - 4 comments

#32 - Support for win32

Issue - State: open - Opened by TommyJW about 6 years ago - 6 comments

#31 - Using without tasks

Issue - State: closed - Opened by TommyJW about 6 years ago - 5 comments

#30 - Added sliding_similarities module with continuous jaccard

Pull Request - State: open - Opened by Avsecz about 6 years ago - 2 comments

#29 - Fixed bug in loading of reverse-complement seqlets

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

#28 - Bugfix for tensorflow backend

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

#27 - Numerical stability fix on min threshold

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

#26 - Migrated to tensorflow backend

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

#25 - tomtom query edge case in `fetch_tomtom_matches`

Issue - State: open - Opened by mhfzsharmin about 6 years ago

#24 - Add random seed as parameter, fix min_seqlet

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

#22 - Bugfix for when len(split_patterns)==0

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

#21 - Error: zero-size array to reduction operation maximum which has no identity

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

#20 - Fix loading when there are no patterns

Pull Request - State: closed - Opened by AvantiShri over 6 years ago - 1 comment

#19 - Changed the default n_cores from 20 to 4

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