saezlab/dorothea issues and pull requests

#74 - run_viper() error

Issue - State: open - Opened by ejfertig 18 days ago

#74 - run_viper() error

Issue - State: open - Opened by ejfertig 18 days ago

#73 - Update README.md

Pull Request - State: closed - Opened by YanshiHu 4 months ago - 2 comments

#73 - Update README.md

Pull Request - State: closed - Opened by YanshiHu 4 months ago - 2 comments

#72 - Update README.md

Pull Request - State: open - Opened by YanshiHu 4 months ago

#72 - Update README.md

Pull Request - State: open - Opened by YanshiHu 4 months ago

#71 - run_viper() ERROR: no method for coercing this S4 class to a vector

Issue - State: open - Opened by sshanyiiii 11 months ago - 2 comments

#71 - run_viper() ERROR: no method for coercing this S4 class to a vector

Issue - State: open - Opened by sshanyiiii 11 months ago - 2 comments

#70 - connection error when retrieve the data

Issue - State: open - Opened by dandancao2023 about 1 year ago - 1 comment

#70 - connection error when retrieve the data

Issue - State: open - Opened by dandancao2023 about 1 year ago - 1 comment

#69 - Error with run_viper wrapper and viper command

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

#69 - Error with run_viper wrapper and viper command

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

#68 - Error in mutate()

Issue - State: closed - Opened by jlx15 almost 2 years ago - 4 comments

#68 - Error in mutate()

Issue - State: closed - Opened by jlx15 almost 2 years ago - 4 comments

#67 - Question regarding input into run_viper()

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

#67 - Question regarding input into run_viper()

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

#66 - No dataframe output when I try to generate Viper score per cell and clusters

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

#66 - No dataframe output when I try to generate Viper score per cell and clusters

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

#65 - Working with Multiome dataset

Issue - State: closed - Opened by sylestiel almost 2 years ago

#65 - Working with Multiome dataset

Issue - State: closed - Opened by sylestiel almost 2 years ago

#64 - Modified DESCRIPTION

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

#64 - Modified DESCRIPTION

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

#63 - Updated vignette

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

#63 - Updated vignette

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

#62 - Fixed logo size

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

#62 - Fixed logo size

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

#61 - Updated docs

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

#61 - Updated docs

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

#60 - The cell annotation need be corrected, after use "dorothea" for FindClusters

Issue - State: closed - Opened by JohnsonHan almost 3 years ago - 1 comment

#60 - The cell annotation need be corrected, after use "dorothea" for FindClusters

Issue - State: closed - Opened by JohnsonHan almost 3 years ago - 1 comment

#59 - Request: tables from Garcia-Alonso et al 2019

Issue - State: closed - Opened by jeremie-le-pen almost 3 years ago

#59 - Request: tables from Garcia-Alonso et al 2019

Issue - State: closed - Opened by jeremie-le-pen almost 3 years ago

#58 - Cluster using the TF regulons

Issue - State: closed - Opened by J1205 almost 3 years ago - 1 comment

#58 - Cluster using the TF regulons

Issue - State: closed - Opened by J1205 almost 3 years ago - 1 comment

#57 - Resulted scaled data

Issue - State: closed - Opened by Tomer9w about 3 years ago - 1 comment

#57 - Resulted scaled data

Issue - State: closed - Opened by Tomer9w about 3 years ago - 1 comment

#56 - Integrated data from seurat

Issue - State: closed - Opened by Chengwei94 about 3 years ago - 1 comment

#56 - Integrated data from seurat

Issue - State: closed - Opened by Chengwei94 about 3 years ago - 1 comment

#55 - No bug, just a question :-)

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

#55 - No bug, just a question :-)

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

#54 - Discrepancy in dataset sizes

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

#54 - Discrepancy in dataset sizes

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

#53 - Release 3 13

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

#53 - Release 3 13

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

#52 - Lazy data

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

#52 - Lazy data

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

#51 - Lazy data

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

#51 - Lazy data

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

#50 - Revert "error on" to warnings in check-bioc.yml

Issue - State: closed - Opened by christianholland over 3 years ago

#50 - Revert "error on" to warnings in check-bioc.yml

Issue - State: closed - Opened by christianholland over 3 years ago

#49 - Scaled data in dorothea

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

#49 - Scaled data in dorothea

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

#48 - NES using DESEQ2

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

#48 - NES using DESEQ2

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

#47 - data set 'dorothea_hs_pancancer' not found

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

#47 - data set 'dorothea_hs_pancancer' not found

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

#46 - Calculating TF scores and inference on SEURAT clusters

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

#46 - Calculating TF scores and inference on SEURAT clusters

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

#45 - Trace back the evidence

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

#45 - Trace back the evidence

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

#44 - Reliability of mode of regulation

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

#44 - Reliability of mode of regulation

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

#43 - Fix mor

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

#43 - Fix mor

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

#42 - Ambigious mor

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

#42 - Ambigious mor

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

#41 - access to dorothea_hs?

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

#41 - access to dorothea_hs?

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

#40 - added spatial experiment handling

Pull Request - State: open - Opened by roramirezf almost 4 years ago - 1 comment

#40 - added spatial experiment handling

Pull Request - State: open - Opened by roramirezf almost 4 years ago - 1 comment

#39 - Integration of regulon activities across different datasets

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

#39 - Integration of regulon activities across different datasets

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

#38 - Added pancancer regulons

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

#38 - Added pancancer regulons

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

#37 - Switch to gh actions

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

#37 - Switch to gh actions

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

#36 - fixed bug in unit tests due to Seurat pkg update

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

#36 - fixed bug in unit tests due to Seurat pkg update

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

#35 - Using ExpressionSet data objects from GEO

Issue - State: closed - Opened by allcatsaregrey about 4 years ago - 3 comments

#35 - Using ExpressionSet data objects from GEO

Issue - State: closed - Opened by allcatsaregrey about 4 years ago - 3 comments

#34 - Preprocessing for Bulk RNA-Seq

Issue - State: closed - Opened by mdmanurung about 4 years ago - 2 comments

#34 - Preprocessing for Bulk RNA-Seq

Issue - State: closed - Opened by mdmanurung about 4 years ago - 2 comments

#33 - TF Enrichment Scores

Issue - State: closed - Opened by jamrute about 4 years ago - 2 comments

#33 - TF Enrichment Scores

Issue - State: closed - Opened by jamrute about 4 years ago - 2 comments

#32 - df2regulon function returns list instead of regulon object

Issue - State: closed - Opened by justinjacobse about 4 years ago - 2 comments

#32 - df2regulon function returns list instead of regulon object

Issue - State: closed - Opened by justinjacobse about 4 years ago - 2 comments

#31 - run_viper input

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

#31 - run_viper input

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

#30 - Retrieve genes used for TF ID

Issue - State: closed - Opened by SuFuBel about 4 years ago - 2 comments

#30 - Retrieve genes used for TF ID

Issue - State: closed - Opened by SuFuBel about 4 years ago - 2 comments

#29 - install error

Issue - State: closed - Opened by ojziff about 4 years ago - 2 comments

#29 - install error

Issue - State: closed - Opened by ojziff about 4 years ago - 2 comments

#28 - Shifted viper package from suggest to depends

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

#28 - Shifted viper package from suggest to depends

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

#27 - Dorothea using "RNA" assay by default instead of providing the option to indicate the real assay to use.

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

#27 - Dorothea using "RNA" assay by default instead of providing the option to indicate the real assay to use.

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

#26 - Update tf census

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

#26 - Update tf census

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

#25 - Problem with object sizes.

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

#25 - Problem with object sizes.

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

GitHub / saezlab/dorothea issues and pull requests