stemangiola/tidySummarizedExperiment issues and pull requests

#99 - Improve performances of select and distinct

Issue - State: open - Opened by stemangiola 2 months ago

#98 - When a dataset if left_joined by .feature, it gets very slow

Issue - State: open - Opened by stemangiola 3 months ago

#97 - Changing how a SumarizedExperiment gets displayed should not be a side effect of loading the package

Issue - State: open - Opened by hpages 5 months ago - 3 comments

#96 - fix bug i introduced

Pull Request - State: closed - Opened by mikelove 9 months ago

#95 - use rwrokflow

Pull Request - State: closed - Opened by stemangiola 9 months ago

#94 - Adding `mutate_features` and `mutate_samples`

Pull Request - State: closed - Opened by mikelove 9 months ago - 6 comments

#93 - Make clear than `n` isn't used?

Issue - State: open - Opened by mikelove 10 months ago - 1 comment

#92 - Robustify utility check

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

#91 - redundant RowData in resultant tibble object

Issue - State: closed - Opened by cparsania 10 months ago - 1 comment

#90 - Group split

Pull Request - State: closed - Opened by B0ydT about 1 year ago - 4 comments

#89 - Make distinct as efficient as select for 20K+ samples

Issue - State: open - Opened by stemangiola about 1 year ago

#88 - Add news file

Pull Request - State: open - Opened by william-hutchison about 1 year ago - 1 comment

#87 - Fix unnest with new purrr

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

#86 - Improve `plot_ly`

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

#85 - replace imap, which is behaving inconsistently

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

#84 - Warning:The assays in your SummarizedExperiment have row names, but they don't agree with the row names of the SummarizedExperiment object itself

Issue - State: open - Opened by artur-sannikov over 1 year ago - 1 comment

#83 - Improve plot_ly

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

#82 - Generalise to 0 dimensions

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

#81 - Update documentation

Pull Request - State: closed - Opened by noriakis over 1 year ago - 8 comments

#80 - Fix checks for duplicated dimnames

Pull Request - State: closed - Opened by csoneson over 1 year ago
Labels: bug, enhancement

#79 - `tidySE` deal with missing assay names

Issue - State: open - Opened by stemangiola over 1 year ago
Labels: bug

#78 - Bugfix nonmatching dimnames

Pull Request - State: closed - Opened by csoneson over 1 year ago - 20 comments
Labels: bug

#77 - Unnest se

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

#76 - Tidy operations with `tidySE` when `colData` and `rowData` share column names

Issue - State: open - Opened by stemangiola over 1 year ago - 5 comments
Labels: bug

#75 - Implement `group_by` and `with_groups` for `tidySummarizedExperiment`

Issue - State: open - Opened by stemangiola over 1 year ago - 1 comment
Labels: enhancement

#74 - Speedup `nest` and `unnest` for massive dataset in `tidySummarizedExperiment`

Issue - State: open - Opened by stemangiola over 1 year ago
Labels: enhancement

#73 - drop exports

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

#72 - drop generics

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

#71 - Unnesting with RangedSummarizedExperiment objects

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

#70 - `tidySE` manage `to_tibble` if rownames not match, or are absent

Issue - State: closed - Opened by sdgamboa almost 2 years ago - 9 comments
Labels: bug, enhancement

#69 - Fix unnesting with RangedSummarizedExperiment objects

Pull Request - State: closed - Opened by william-hutchison almost 2 years ago - 2 comments

#68 - unnesting on RangedSummarizedExperiment cols

Issue - State: closed - Opened by mikelove almost 2 years ago - 6 comments

#67 - Fix mutate assay

Pull Request - State: closed - Opened by stemangiola almost 2 years ago

#66 - mutate() shifts order of data

Issue - State: closed - Opened by mikelove almost 2 years ago - 12 comments

#65 - Fix tidyr

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

#64 - unexpected output when using filter function

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

#63 - Dev

Pull Request - State: closed - Opened by stemangiola over 2 years ago

#62 - dplyr::arrange function?

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

#61 - Fix typo

Pull Request - State: closed - Opened by mblue9 over 2 years ago

#60 - Fix column header

Pull Request - State: closed - Opened by stemangiola over 2 years ago

#59 - Optimise nest

Pull Request - State: closed - Opened by stemangiola over 2 years ago

#58 - Dev

Pull Request - State: closed - Opened by stemangiola over 2 years ago

#57 - make filter more robust

Pull Request - State: closed - Opened by stemangiola over 2 years ago

#56 - convert delayedArray to Matrix before printing

Pull Request - State: closed - Opened by stemangiola over 2 years ago

#55 - improve efficiency of often-used functions for huge datasets (2k samp…

Pull Request - State: closed - Opened by stemangiola over 2 years ago

#54 - small edits

Pull Request - State: closed - Opened by stemangiola over 2 years ago

#53 - slice using a range doesn't work on ungrouped data

Issue - State: open - Opened by mblue9 over 2 years ago

#52 - If only one assay is present and is nameless, the assay column is not printed

Issue - State: open - Opened by stemangiola over 2 years ago - 2 comments

#51 - Few updates and fixes for docs

Pull Request - State: closed - Opened by mblue9 over 2 years ago

#50 - Add workaround for git change

Pull Request - State: closed - Opened by mblue9 over 2 years ago

#49 - update_action_to_bioc_3.15

Pull Request - State: closed - Opened by mblue9 over 2 years ago - 5 comments

#48 - Dev

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

#47 - Update to Bioc 3.14 and R 4.1

Pull Request - State: closed - Opened by mblue9 about 3 years ago - 3 comments

#46 - Dev

Pull Request - State: closed - Opened by stemangiola about 3 years ago

#45 - Adapt to ranged se

Pull Request - State: closed - Opened by stemangiola about 3 years ago

#44 - Dev

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

#43 - Speed up nest

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

#42 - Error: Key columns are missing. A data frame is returned for independent data analysis

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

#41 - Update DESCRIPTION

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

#40 - rebase

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

#39 - Dev

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

#38 - fix print for singleCellExperiment

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

#37 - failure when RangedSummarizedExperiment has named rowRanges that also include "ID" mcol

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

#36 - Dev

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

#35 - Understand when I should put warning is using complex non-optimisable operations

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

#34 - Tcga maria

Pull Request - State: closed - Opened by stemangiola over 3 years ago - 15 comments