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GitHub / saezlab/omnipath issues and pull requests

#61 - pip install omnipath does not install the package properly

Issue - State: open - Opened by elmbeech about 2 months ago - 4 comments

#60 - Inherit request settings to avoid certificate issues

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

#57 - Incompatibility with Numpy >= 2

Issue - State: closed - Opened by pablormier 8 months ago - 6 comments

#56 - Bump version?

Issue - State: closed - Opened by pauleve 9 months ago - 1 comment

#55 - Metadata for all the OmniPath databases.

Issue - State: open - Opened by ecarrenolozano 10 months ago

#54 - Incompatibility of ``pybiomart`` and ``omnipath``

Issue - State: closed - Opened by PauBadiaM over 1 year ago - 3 comments

#53 - Programmatically fix database version downloaded

Issue - State: open - Opened by bednarsky over 1 year ago

#52 - Collectri issue with loops

Issue - State: closed - Opened by dbdimitrov over 1 year ago - 2 comments

#51 - Open position in the development of omnipath / pypath / biocypher

Issue - State: closed - Opened by iulusoy over 1 year ago - 2 comments

#50 - Networking issue around package load manifests as a param validation error

Issue - State: closed - Opened by yulicarp about 2 years ago - 14 comments
Labels: enhancement

#49 - How to get data on the interactions of all receptor ligands?

Issue - State: closed - Opened by qijt123 about 2 years ago - 1 comment

#48 - Fix/tests

Pull Request - State: closed - Opened by michalk8 about 2 years ago - 1 comment

#47 - Query on change in number of interactions

Issue - State: closed - Opened by Tama-sha about 2 years ago - 2 comments
Labels: question

#46 - dc.get_resource('PanglaoDB') error

Issue - State: closed - Opened by zhaleh-safikhani about 2 years ago - 1 comment
Labels: bug

#45 - omnipath support for python3.11?

Issue - State: closed - Opened by benwilks about 2 years ago
Labels: bug

#44 - TypeError: read_csv() got an unexpected keyword argument 'squeeze'

Issue - State: closed - Opened by shreyaslabh about 2 years ago - 1 comment
Labels: bug

#43 - Uniprot IDs to Gene symbols

Issue - State: closed - Opened by Coaasim about 2 years ago - 6 comments
Labels: question

#42 - Orthology conversion via homologene

Pull Request - State: closed - Opened by dbdimitrov about 2 years ago - 2 comments

#41 - get_resource MSigDB fails with read_csv() error due to unexpected argument 'squeeze'

Issue - State: closed - Opened by pcm32 over 2 years ago - 1 comment
Labels: bug

#40 - Fix/pandas-read

Pull Request - State: closed - Opened by michalk8 over 2 years ago
Labels: bug

#39 - TypeError: read_csv() got an unexpected keyword argument 'squeeze'

Issue - State: closed - Opened by slobentanzer over 2 years ago - 1 comment
Labels: bug

#38 - omnipath throwing error perhaps because of new pandas version?

Issue - State: closed - Opened by LLehner over 2 years ago

#37 - Add annotations to network data frames

Issue - State: open - Opened by deeenes over 2 years ago
Labels: enhancement

#36 - Support for custom interaction attributes

Issue - State: open - Opened by deeenes over 2 years ago
Labels: enhancement

#35 - "ChunkedEncodingError" when running dc.get_resource('MSigDB')

Issue - State: closed - Opened by alexandregrimaldi over 2 years ago - 1 comment

#34 - RetryError when run get_resource(‘MSigDB’)

Issue - State: closed - Opened by ChangLu92 over 2 years ago - 2 comments
Labels: server side

#32 - Issues downloading annotation resources

Issue - State: closed - Opened by PauBadiaM over 2 years ago - 1 comment
Labels: server side

#31 - Fix badges

Pull Request - State: closed - Opened by michalk8 over 2 years ago - 1 comment

#30 - How can I verify pathways linked to a specific ligand/receptor or protein/protein interaction?

Issue - State: closed - Opened by mgrantpeters over 2 years ago - 1 comment
Labels: question

#29 - Feature/update ci

Pull Request - State: closed - Opened by michalk8 almost 3 years ago - 1 comment

#28 - Release current version?

Issue - State: closed - Opened by simonvh almost 3 years ago - 5 comments

#27 - Conda package

Issue - State: closed - Opened by LuckyMD almost 3 years ago - 2 comments
Labels: question

#26 - source, target, ligand and receptor

Issue - State: closed - Opened by wangjiawen2013 almost 3 years ago - 1 comment
Labels: question

#25 - omnipath connection on Amazon web service and my PC

Issue - State: closed - Opened by sophieRAIBAUD about 3 years ago - 5 comments
Labels: SSL

#24 - Meaning behind "consensus_direction"

Issue - State: closed - Opened by pokedthefrog about 3 years ago - 7 comments
Labels: question

#23 - set species

Issue - State: closed - Opened by wangjiawen2013 about 3 years ago - 2 comments
Labels: question

#22 - Add "small_molecule" as valid interaction dataset

Pull Request - State: closed - Opened by pokedthefrog over 3 years ago - 1 comment
Labels: enhancement

#21 - Copy new intercell related procedures from the R package

Issue - State: open - Opened by deeenes over 3 years ago
Labels: enhancement

#20 - Question: interactions erroneously reversed in some cases?

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

#19 - fix for #18

Pull Request - State: closed - Opened by TheAustinator over 3 years ago - 2 comments

#17 - omnipath tutorials

Issue - State: open - Opened by wangjiawen2013 over 3 years ago - 3 comments
Labels: question

#16 - Interaction annotations by pair, not individual genes

Issue - State: closed - Opened by dnjst over 3 years ago - 2 comments
Labels: question

#15 - Pivot annotations

Pull Request - State: closed - Opened by deeenes over 3 years ago
Labels: enhancement

#14 - Update release notes, CI, add badge

Pull Request - State: closed - Opened by michalk8 almost 4 years ago - 1 comment

#13 - Remove enum tools

Pull Request - State: closed - Opened by michalk8 almost 4 years ago - 1 comment

#12 - Run Omnipath on a VM

Issue - State: closed - Opened by DriessenA about 4 years ago - 1 comment

#11 - Some resources not included in last Omnipath version?

Issue - State: closed - Opened by Jordi-Valls about 4 years ago - 3 comments
Labels: question

#10 - Fix writing empty values in cache

Pull Request - State: closed - Opened by michalk8 about 4 years ago

#9 - Update ci

Pull Request - State: closed - Opened by michalk8 about 4 years ago - 1 comment

#8 - Error when importing omnipath?

Issue - State: closed - Opened by jadeshi over 4 years ago - 1 comment
Labels: wontfix

#5 - Add post trans (#5)

Pull Request - State: closed - Opened by michalk8 over 4 years ago

#4 - Add post trans

Pull Request - State: closed - Opened by michalk8 over 4 years ago

#3 - Fixes

Pull Request - State: closed - Opened by michalk8 over 4 years ago - 2 comments

#2 - Major refactoring

Pull Request - State: closed - Opened by michalk8 over 4 years ago - 4 comments

#1 - First version of omnipath

Pull Request - State: closed - Opened by michalk8 over 4 years ago - 2 comments