kipoi/kipoi-veff issues and pull requests

#46 - How can I use the "ax=None" in the plot_mutmap function?

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

#45 - Getting a NotImplementedError: "sortBed" does not appear to be installed or on the path... error when running score_variants

Issue - State: open - Opened by sukritikumar4 over 2 years ago - 1 comment

#44 - compatability issues with installation of deepsea

Issue - State: open - Opened by cmlakhan over 3 years ago - 1 comment

#43 - Fix a bug when ALT is empty

Pull Request - State: open - Opened by s6juncheng over 3 years ago

#42 - Update dev-requirements-py36.yml - freeze pandas version

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

#41 - Update mutators.py

Pull Request - State: open - Opened by Avsecz over 4 years ago

#40 - Simple change to make tqdm progress more notebook friendly

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

#39 - Typo fix for the error message in score.py

Pull Request - State: closed - Opened by gokceneraslan over 4 years ago - 1 comment

#38 - Results differ unexpectedly between `pipeline.predict` and `query_bed` with `ref` score

Issue - State: open - Opened by an1lam over 4 years ago - 6 comments
Labels: help wanted

#37 - Update .circleci/config.yml

Pull Request - State: closed - Opened by Avsecz over 4 years ago - 5 comments

#36 - Fix `MutationMap.query_bed`

Pull Request - State: closed - Opened by an1lam over 4 years ago - 9 comments

#35 - Fix typo in mutation map instructions

Pull Request - State: closed - Opened by an1lam over 4 years ago - 1 comment

#34 - dataloader_args

Issue - State: closed - Opened by ggabernet almost 5 years ago - 2 comments

#33 - Bump version: 0.2.3 → 0.3.0

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

#32 - Niceparse

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

#31 - Bump version: 0.2.2 → 0.2.3

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

#30 - Dependencies: Using kipoi_utils

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

#29 - fix None handling for ID=.

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

#28 - Update setup.py

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

#27 - Speedup writing to file

Issue - State: open - Opened by Avsecz over 5 years ago - 1 comment

#26 - added --singularity to score_variants

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

#25 - options to show ref_seq, box ref allele

Pull Request - State: closed - Opened by s6juncheng over 5 years ago

#24 - fix logging

Pull Request - State: closed - Opened by krrome over 5 years ago - 1 comment
Labels: in progress

#23 - Kipoi-veff fails silently when the input files don't exist

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

#22 - Add logit_diff scoring function.

Issue - State: open - Opened by Avsecz over 5 years ago

#21 - Write buffer

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

#20 - Error when chromosome names don't start with `chr`

Issue - State: open - Opened by Avsecz over 5 years ago - 1 comment

#19 - batch-writing to the vcf file

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

#18 - No error message if the input file doesn't exist

Issue - State: closed - Opened by dansimancas over 5 years ago - 1 comment

#17 - Use HDF5BatchWriter instead of deepdish when writing the results for hdf5 files

Issue - State: open - Opened by Avsecz over 5 years ago

#16 - Comply with dl repo

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

#15 - Comply with dl repo + allow bed row index as variant index

Pull Request - State: closed - Opened by krrome almost 6 years ago - 2 comments

#14 - update ModelInfoExtractor

Issue - State: closed - Opened by krrome almost 6 years ago - 1 comment

#13 - updated docs

Pull Request - State: closed - Opened by Avsecz almost 6 years ago - 1 comment

#12 - Docs improvement

Issue - State: open - Opened by Avsecz almost 6 years ago

#11 - create tempfile. closes #10

Pull Request - State: closed - Opened by Avsecz almost 6 years ago - 1 comment

#10 - Make a duplicate of variants.vcf when testing

Issue - State: closed - Opened by krrome almost 6 years ago - 2 comments
Labels: bug

#9 - restrict version to kipoi >=0.4

Issue - State: open - Opened by Avsecz almost 6 years ago

#8 - allow `stdout` filename on score_variants

Issue - State: open - Opened by Avsecz almost 6 years ago