churchmanlab/genewalk issues and pull requests

#76 - Update link to PC12 resource

Pull Request - State: closed - Opened by bgyori 2 months ago - 1 comment

#75 - gzip.BadGzipFile: Not a gzipped file (b'<!') | pandas.errors.EmptyDataError: No columns to parse from file

Issue - State: closed - Opened by Cameron-Nguyen1 2 months ago - 1 comment

#74 - Update URLs to HTTPS

Pull Request - State: closed - Opened by bgyori 5 months ago

#73 - extending to KEGG

Issue - State: closed - Opened by lli-rice 5 months ago - 1 comment

#71 - Add .readthedocs.yaml file

Pull Request - State: closed - Opened by ri23 about 1 year ago

#70 - Problem with genewalk

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

#69 - Update2023

Pull Request - State: closed - Opened by ri23 over 1 year ago

#68 - AttributeError: module 'typing' has no attribute 'NoReturn

Issue - State: closed - Opened by ri23 over 2 years ago - 3 comments

#61 - Use comment instead of skiprows when loading GOA

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

#60 - GO annotations file comment rows have changed

Issue - State: closed - Opened by bgyori over 3 years ago - 1 comment

#49 - Code for regulator/moonlighter plots

Issue - State: closed - Opened by npokorzynski over 3 years ago - 4 comments

#48 - Mouse ids are not working with genewalk?

Issue - State: closed - Opened by Anara2018 over 3 years ago - 1 comment

#47 - Limit gensim version to < 4 for compatibility

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

#46 - Error when calling word2vec: unexpected keyword argument 'size'

Issue - State: closed - Opened by ri23 over 3 years ago - 2 comments

#45 - GO Terms

Issue - State: closed - Opened by npokorzynski over 3 years ago - 1 comment

#44 - Trouble Using GeneWalk

Issue - State: closed - Opened by SinjaFan over 3 years ago - 2 comments

#43 - Test CLI directly

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

#42 - INDRA script generation

Issue - State: closed - Opened by xandmac over 3 years ago - 2 comments

#41 - Enable GeneWalk to run on non-human-mapped gene IDs and networks

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

#40 - Extend support for custom SIF input networks

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

#39 - Test with and without INDRA

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

#38 - Add support for rat gene lists using RGD

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

#37 - No regulators identified?

Issue - State: closed - Opened by npokorzynski over 3 years ago - 4 comments

#36 - Integrate HGNC resources

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

#35 - Add rows for genes with no GO annotations to results spreadsheet

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

#34 - IndexError: list index out of range

Issue - State: closed - Opened by eskederks over 3 years ago - 2 comments

#33 - Criteria for barplot output

Issue - State: closed - Opened by npokorzynski over 3 years ago - 8 comments

#32 - AttributeError: type object 'object' has no attribute 'dtype'

Issue - State: closed - Opened by vertesy over 3 years ago - 2 comments

#31 - Install issue

Issue - State: closed - Opened by npokorzynski over 3 years ago - 8 comments

#30 - network source file

Issue - State: closed - Opened by amitpande74 over 3 years ago - 4 comments

#29 - Illustration of the GeneWalk network

Issue - State: closed - Opened by izu0421 over 3 years ago - 4 comments

#28 - Installation failed.

Issue - State: closed - Opened by alhafidzhamdan over 3 years ago - 6 comments

#27 - Rat genome

Issue - State: closed - Opened by amitpande74 over 3 years ago - 1 comment

#26 - rdflib=4.2.2 and python 3 version conflict

Issue - State: closed - Opened by tmargus over 3 years ago - 2 comments

#25 - ML

Issue - State: closed - Opened by Vashar20 over 3 years ago - 1 comment

#24 - Don't download all resources up front

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

#23 - Add end-to-end test for CLI

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

#22 - Plotly

Pull Request - State: closed - Opened by ri23 over 3 years ago

#21 - Generate plots for results

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

#20 - Increase Python version requirement and move testing

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

#19 - Adapt to INDRA v18

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

#18 - Entrez

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

#17 - ensembl_id

Issue - State: closed - Opened by marttine almost 5 years ago - 1 comment

#16 - Error while downloading resources - PathwayCommons11.All.hgnc.sif.gz

Issue - State: closed - Opened by leiendeckerlu almost 5 years ago - 7 comments

#15 - compiling the resource folder - error

Issue - State: closed - Opened by jrconner16 almost 5 years ago - 8 comments

#14 - Importing the numpy c-extensions failed.

Issue - State: closed - Opened by gitpycode almost 5 years ago

#13 - Handle Ensembl ID suffixes and error if ID mapping failed

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

#12 - Ensembl IDs with dots cause problems

Issue - State: closed - Opened by chrarnold about 5 years ago - 4 comments

#11 - Start testing on Travis

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

#10 - Visualization of the results

Issue - State: closed - Opened by chrarnold about 5 years ago - 7 comments

#9 - Fix handling Ensembl IDs in perform statistics

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

#8 - KeyError: 'ensembl_id'

Issue - State: closed - Opened by chrarnold about 5 years ago - 3 comments

#7 - Add version to CLI

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

#6 - version argument missing

Issue - State: closed - Opened by chrarnold about 5 years ago

#5 - Support Ensembl ID lists

Pull Request - State: closed - Opened by bgyori about 5 years ago - 3 comments

GitHub / churchmanlab/genewalk issues and pull requests