stemangiola/tidysinglecellexperiment issues and pull requests

#112 - fixes to aggregate and as_SE

Pull Request - State: closed - Opened by stemangiola 16 days ago

#111 - add check for duplicated rows for `aggregate_cells`

Issue - State: open - Opened by stemangiola 16 days ago

#110 - aggregate_cells takes too long

Issue - State: open - Opened by MaximilianNuber 3 months ago - 2 comments

#109 - Path of images of stemangiola.github.io/tidySingleCellExperimen not correct

Issue - State: open - Opened by corinabioinformatic 4 months ago

#108 - [feature request] use cli printing

Issue - State: open - Opened by stemangiola 4 months ago

#107 - feature request: join_features shape="long" should carry the rowData as well, similarly to `tidySummarizedExperiment`

Issue - State: open - Opened by stemangiola 4 months ago

#106 - update nest to use cell numeric id rather than original id which can …

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

#105 - R dependency

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

#104 - Fix aggregate with rowdata

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

#103 - Issue 9 colore view only

Pull Request - State: open - Opened by qclayssen 9 months ago

#102 - fix-biocCHECK

Pull Request - State: closed - Opened by stemangiola 11 months ago

#100 - Improve `plot_ly`

Pull Request - State: closed - Opened by william-hutchison 11 months ago

#99 - Refactor *_join functions with function factory

Pull Request - State: closed - Opened by lambdamoses 12 months ago - 1 comment

#98 - Allow y as S4 DataFrame in *_join()

Pull Request - State: closed - Opened by lambdamoses 12 months ago - 5 comments

#97 - group_split

Pull Request - State: closed - Opened by B0ydT 12 months ago - 10 comments

#96 - Improve plot_ly

Pull Request - State: closed - Opened by william-hutchison 12 months ago - 9 comments

#95 - Clarifications about `.abundance_counts`

Issue - State: open - Opened by denvercal1234GitHub about 1 year ago - 4 comments

#94 - Improve documentation

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

#93 - Inconsistency between assay data used and what is advised in SingleR?

Issue - State: closed - Opened by denvercal1234GitHub about 1 year ago - 10 comments

#92 - Error from plotting `sce` object: '.abundance_counts' not found

Issue - State: closed - Opened by denvercal1234GitHub about 1 year ago - 9 comments

#91 - Clarification of getting back/disabling the viewing of sce as tibble?

Issue - State: closed - Opened by denvercal1234GitHub about 1 year ago - 2 comments

#90 - Add slice functions

Pull Request - State: closed - Opened by noriakis about 1 year ago - 3 comments
Labels: enhancement

#89 - Add conditional print method for objects that contain alternative experiments

Pull Request - State: open - Opened by Biomiha about 1 year ago - 37 comments

#88 - `tidySCE`: `slice` masks tidyverse::slice

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

#87 - add argument to aggregate_cells

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

#86 - Speedup aggregate cells

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

#85 - Tweak print method to show altExpNames

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

#84 - `tidySCE` Speedup aggregate_cells

Issue - State: closed - Opened by stemangiola about 1 year ago - 2 comments
Labels: enhancement

#83 - cleaning `BiocCheck()`; linting revision; GHA bump to Bioc devel

Pull Request - State: closed - Opened by HelenaLC about 1 year ago
Labels: enhancement

#82 - `tidySCE` deal with missing assay names

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

#81 - `tidySCE` Functionality to see and access the altExp slot

Issue - State: open - Opened by Biomiha about 1 year ago - 18 comments
Labels: enhancement

#80 - Method for S4 DataFrame for left_join

Issue - State: closed - Opened by lambdamoses about 1 year ago - 17 comments

#79 - revise unit tests `tidySingleCellExperiment`

Pull Request - State: closed - Opened by HelenaLC about 1 year ago - 9 comments
Labels: bug, enhancement

#78 - update README and Vignette

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

#77 - +@name tags; +missing doc for inner_join

Pull Request - State: closed - Opened by HelenaLC about 1 year ago - 3 comments

#76 - add @name back

Pull Request - State: closed - Opened by stemangiola about 1 year ago - 3 comments
Labels: bug

#75 - doc revision

Pull Request - State: closed - Opened by HelenaLC about 1 year ago - 1 comment
Labels: documentation

#74 - method documentation & vignette revision

Pull Request - State: closed - Opened by HelenaLC about 1 year ago - 9 comments

#73 - prettifying vignette revision (formatting, hyperlinks etc.)

Pull Request - State: closed - Opened by HelenaLC about 1 year ago - 5 comments

#71 - Implement `group_by` and `with_groups` for `tidySingleCellExperiment` and `tidyseurat`

Issue - State: open - Opened by stemangiola about 1 year ago - 15 comments
Labels: enhancement

#70 - Speed up `nest` and `unnest` for massive datasets in `tidySingleCellExperiment`

Issue - State: open - Opened by stemangiola about 1 year ago - 3 comments
Labels: enhancement

#69 - drop exports

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

#68 - Drop bind generics

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

#67 - Add `summarize` as an explicit alias of the function `summarise`

Pull Request - State: closed - Opened by william-hutchison over 1 year ago - 3 comments

#66 - speed up as_tibble in case I have nested columns in the metadata e.g. TCR

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

#65 - add join_by function from dplyr

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

#64 - Use generic aggregate cells from ttservice

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

#63 - adapt aggregate_features() to tidyseurat which is based on ttservice

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

#62 - Consider adding summarize.SingleCellExperiment as an explicit alias of summarise.SingleCellExperiment

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

#61 - Repo website link is broken

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

#60 - Bug when using `joinFeatures` + `SingleCellExperiment` with 1 cell

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

#59 - Added aggregate cells function to README and vignette

Pull Request - State: closed - Opened by william-hutchison over 1 year ago - 2 comments

#58 - Adding aggregate_cells in README and Vignette

Issue - State: closed - Opened by stemangiola over 1 year ago
Labels: documentation

#57 - Added aggregate cells function and dependencies

Pull Request - State: closed - Opened by william-hutchison over 1 year ago - 3 comments

#56 - subsample sce object based on factor in colData

Issue - State: open - Opened by baj12 over 1 year ago - 1 comment

#55 - Add count drop generics

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

#54 - add aggregate_cells

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

#53 - fix tidyr

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

#52 - Fix unique special columns

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

#51 - fix as_meta_data

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

#50 - Make assay output shorter

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

#49 - README has an incredibly long assay(pbmc_small_tidy)

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

#48 - join_features doesn't allow choosing which assay when multiple present

Issue - State: closed - Opened by mblue9 about 2 years ago - 1 comment

#47 - Print hotifx

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

#46 - Fix README

Pull Request - State: closed - Opened by mblue9 about 2 years ago - 1 comment

#45 - options("restore_SingleCellExperiment_show" = FALSE)` doesn't work?

Issue - State: closed - Opened by mblue9 about 2 years ago - 3 comments

#44 - Update Depends R version to 4.1

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

#43 - Installation error with latest (1.7.2) in R 4.0.1: ERROR: unable to collate and parse R files for package ‘tidySingleCellExperiment’

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

#42 - Update github action to Bioc 3.15

Pull Request - State: closed - Opened by mblue9 over 2 years ago - 1 comment

#41 - Print hotifx

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

#40 - Update action to bioc 3.14

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

#39 - deprecate cell column

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

#38 - as_tibble() and slice_sample() cannot handle a column named $cell

Issue - State: closed - Opened by ttriche almost 3 years ago - 4 comments
Labels: enhancement

#37 - Dev

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

#36 - use ttservice

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

#35 - Dev

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

#34 - add dedicated function for tibble objects

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

#33 - update RELEASE 3_13

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

#32 - Dev

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

#31 - drop class and tidy method. This disruptive change is because the pac…

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

#30 - add code and tests

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