databio/cocoa issues and pull requests

#55 - Speed up COCOA and HIS method

Pull Request - State: open - Opened by kinganimz 10 months ago

#54 - HIS method

Pull Request - State: closed - Opened by kinganimz 10 months ago

#54 - HIS method

Pull Request - State: closed - Opened by kinganimz 10 months ago

#53 - Fix runCOCOAPerm function (HIS case)

Issue - State: closed - Opened by kinganimz 11 months ago

#53 - Fix runCOCOAPerm function (HIS case)

Issue - State: closed - Opened by kinganimz 11 months ago

#52 - Speed up COCOA for HIS method

Issue - State: closed - Opened by kinganimz 12 months ago - 1 comment

#52 - Speed up COCOA for HIS method

Issue - State: closed - Opened by kinganimz 12 months ago - 1 comment

#51 - Test runCOCOAPerm in case of HIS

Issue - State: closed - Opened by kinganimz 12 months ago

#50 - Test runCOCOA

Issue - State: closed - Opened by kinganimz 12 months ago

#50 - Test runCOCOA

Issue - State: closed - Opened by kinganimz 12 months ago

#49 - Problem with returning a matrix of appropriate dimensions using the HIS method

Issue - State: closed - Opened by kinganimz 12 months ago

#49 - Problem with returning a matrix of appropriate dimensions using the HIS method

Issue - State: closed - Opened by kinganimz 12 months ago

#48 - HIS method

Issue - State: closed - Opened by kinganimz about 1 year ago

#47 - Problem with region sets annotation

Issue - State: closed - Opened by kinganimz about 1 year ago

#46 - Problem with running ATAC-seq data

Issue - State: closed - Opened by kinganimz about 1 year ago

#46 - Problem with running ATAC-seq data

Issue - State: closed - Opened by kinganimz about 1 year ago

#45 - Create one results table

Issue - State: closed - Opened by kinganimz about 1 year ago - 2 comments

#45 - Create one results table

Issue - State: closed - Opened by kinganimz about 1 year ago - 2 comments

#44 - Problem with 1-column data; convertToFromNullDist function

Issue - State: closed - Opened by kinganimz about 1 year ago

#44 - Problem with 1-column data; convertToFromNullDist function

Issue - State: closed - Opened by kinganimz about 1 year ago

#43 - Supervised COCOA: runCOCOAPerm function

Issue - State: closed - Opened by kinganimz about 1 year ago

#43 - Supervised COCOA: runCOCOAPerm function

Issue - State: closed - Opened by kinganimz about 1 year ago

#42 - The output should be better unified

Issue - State: closed - Opened by kinganimz over 1 year ago - 1 comment

#42 - The output should be better unified

Issue - State: closed - Opened by kinganimz over 1 year ago - 1 comment

#41 - runCOCOAPerm function in case of supervised approach

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

#41 - runCOCOAPerm function in case of supervised approach

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

#40 - Dev

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

#40 - Dev

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

#39 - Matrix

Pull Request - State: open - Opened by nsheff over 1 year ago

#39 - Matrix

Pull Request - State: open - Opened by nsheff over 1 year ago

#38 - merge master with matrix

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

#38 - merge master with matrix

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

#37 - Dev

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

#37 - Dev

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

#36 - Repeatedly checking of input

Issue - State: closed - Opened by nsheff almost 4 years ago

#36 - Repeatedly checking of input

Issue - State: closed - Opened by nsheff almost 4 years ago

#35 - COCOA should just handle the permutations without user intervention

Issue - State: closed - Opened by nsheff almost 4 years ago

#35 - COCOA should just handle the permutations without user intervention

Issue - State: closed - Opened by nsheff almost 4 years ago

#34 - Duplicated information in documentation

Issue - State: closed - Opened by nsheff almost 4 years ago - 1 comment

#34 - Duplicated information in documentation

Issue - State: closed - Opened by nsheff almost 4 years ago - 1 comment

#33 - Too much information in documentation

Issue - State: closed - Opened by nsheff almost 4 years ago - 1 comment

#33 - Too much information in documentation

Issue - State: closed - Opened by nsheff almost 4 years ago - 1 comment

#32 - Vignette structure

Issue - State: closed - Opened by nsheff almost 4 years ago - 1 comment

#31 - Speed up COCOA with matrix operations

Issue - State: open - Opened by j-lawson almost 4 years ago

#30 - Running COCOA on multiple processors

Issue - State: open - Opened by nsheff almost 4 years ago

#30 - Running COCOA on multiple processors

Issue - State: open - Opened by nsheff almost 4 years ago

#29 - COCOA results should be annotated

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

#29 - COCOA results should be annotated

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

#28 - Better approach for detecting single base data

Issue - State: closed - Opened by nsheff almost 4 years ago - 1 comment

#28 - Better approach for detecting single base data

Issue - State: closed - Opened by nsheff almost 4 years ago - 1 comment

#27 - Running outputs prints

Issue - State: closed - Opened by nsheff almost 4 years ago - 1 comment

#27 - Running outputs prints

Issue - State: closed - Opened by nsheff almost 4 years ago - 1 comment

#26 - More informative error message for bad input

Issue - State: closed - Opened by nsheff almost 4 years ago - 1 comment

#25 - targetVar can't be a data.table

Issue - State: closed - Opened by nsheff almost 4 years ago - 1 comment

#25 - targetVar can't be a data.table

Issue - State: closed - Opened by nsheff almost 4 years ago - 1 comment

#24 - COCOA updates

Issue - State: closed - Opened by j-lawson about 4 years ago

#24 - COCOA updates

Issue - State: closed - Opened by j-lawson about 4 years ago

#23 - Add ATAC-seq capabilities to dev

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

#23 - Add ATAC-seq capabilities to dev

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

#22 - Standardize expected inputs and check if inputs are correct

Issue - State: closed - Opened by j-lawson over 5 years ago

#22 - Standardize expected inputs and check if inputs are correct

Issue - State: closed - Opened by j-lawson over 5 years ago

#21 - merge updates

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

#21 - merge updates

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

#20 - averagePerRegion for ATAC

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

#20 - averagePerRegion for ATAC

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

#19 - Synthetic/real ATAC-seq data to include with package

Issue - State: closed - Opened by j-lawson over 5 years ago

#18 - Small vignette for ATAC data

Issue - State: closed - Opened by j-lawson over 5 years ago

#18 - Small vignette for ATAC data

Issue - State: closed - Opened by j-lawson over 5 years ago

#17 - Make sure ATAC-seq data works in visualization functions

Issue - State: closed - Opened by j-lawson over 5 years ago

#17 - Make sure ATAC-seq data works in visualization functions

Issue - State: closed - Opened by j-lawson over 5 years ago

#16 - Unit tests for ATAC-seq data and new scoring methods

Issue - State: closed - Opened by j-lawson over 5 years ago

#16 - Unit tests for ATAC-seq data and new scoring methods

Issue - State: closed - Opened by j-lawson over 5 years ago

#15 - bug fixes

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

#14 - SignalAlongPC error when using ATACseq data

Issue - State: closed - Opened by AlexWixom over 5 years ago - 7 comments

#14 - SignalAlongPC error when using ATACseq data

Issue - State: closed - Opened by AlexWixom over 5 years ago - 7 comments

#13 - cocoa-net

Issue - State: closed - Opened by nsheff about 6 years ago - 1 comment

#13 - cocoa-net

Issue - State: closed - Opened by nsheff about 6 years ago - 1 comment

#12 - Updates for BIOC release

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

#12 - Updates for BIOC release

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

#11 - Dev

Pull Request - State: closed - Opened by j-lawson about 6 years ago - 2 comments

#11 - Dev

Pull Request - State: closed - Opened by j-lawson about 6 years ago - 2 comments

#10 - Dev

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

#9 - Update README

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

#8 - Updates for Bioconductor review and new scope of package

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

#7 - Update plotting functions and documentation

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

#6 - A few more updates for Bioc standards

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

#5 - Updates for Bioconductor submission

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

#4 - Update docs and fix some warnings

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

#3 - docs and website

Issue - State: closed - Opened by nsheff over 6 years ago - 5 comments

#2 - Update dev

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

#1 - Standardize names of parameters

Issue - State: closed - Opened by j-lawson over 6 years ago

GitHub / databio/cocoa issues and pull requests