stemangiola/tidySingleCellExperiment

Issues

• aggregate_cells takes too long

  #110 opened 6 months ago by MaximilianNuber
  2

• Path of images of stemangiola.github.io/tidySingleCellExperimen not correct

  #109 opened 6 months ago by corinabioinformatic
  0

• [feature request] use cli printing

  #108 opened 7 months ago by stemangiola
  0

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

  #107 opened 7 months ago by stemangiola
  0

• Method for S4 DataFrame for left_join

  #80 opened a year ago by lambdamoses
  17

• Implement `group_by` and `with_groups` for `tidySingleCellExperiment` and `tidyseurat`

  #71 opened a year ago by stemangiola
  15

• Clarifications about `.abundance_counts`

  #95 opened a year ago by denvercal1234GitHub
  4

• Clarification of getting back/disabling the viewing of sce as tibble?

  #91 opened a year ago by denvercal1234GitHub
  2

• Error from plotting `sce` object: '.abundance_counts' not found

  #92 opened a year ago by denvercal1234GitHub
  9

• Inconsistency between assay data used and what is advised in SingleR?

  #93 opened a year ago by denvercal1234GitHub
  10

• `tidySCE` Speedup aggregate_cells

  #84 opened a year ago by stemangiola
  2

• `tidySCE`: `slice` masks tidyverse::slice

  #88 opened a year ago by stemangiola
  0

• `tidySCE` Functionality to see and access the altExp slot

  #81 opened a year ago by Biomiha
  18

• add join_by function from dplyr

  #65 opened a year ago by stemangiola
  0

• `tidySCE` deal with missing assay names

  #82 opened a year ago by stemangiola
  0

• Speed up `nest` and `unnest` for massive datasets in `tidySingleCellExperiment`

  #70 opened a year ago by stemangiola
  3

• try to not re-declare generics

  #23 opened a year ago by stemangiola
  0

• Consider adding summarize.SingleCellExperiment as an explicit alias of summarise.SingleCellExperiment

  #62 opened 2 years ago by keyes-timothy
  1

• speed up as_tibble in case I have nested columns in the metadata e.g. TCR

  #66 opened 2 years ago by stemangiola
  0

• adapt aggregate_features() to tidyseurat which is based on ttservice

  #63 opened 2 years ago by stemangiola
  3

• Bug when using `joinFeatures` + `SingleCellExperiment` with 1 cell

  #60 opened 2 years ago by multimeric
  1

• Repo website link is broken

  #61 opened 2 years ago by multimeric
  3

• Adding aggregate_cells in README and Vignette

  #58 opened 2 years ago by stemangiola
  0

• README has an incredibly long assay(pbmc_small_tidy)

  #49 opened 2 years ago by stemangiola
  2

• subsample sce object based on factor in colData

  #56 opened 2 years ago by baj12
  1

• add aggregate_cells

  #54 opened 2 years ago by stemangiola
  0

• options("restore_SingleCellExperiment_show" = FALSE)` doesn't work?

  #45 opened 2 years ago by mblue9
  3

• join_features doesn't allow choosing which assay when multiple present

  #48 opened 2 years ago by mblue9
  1

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

  #43 opened 2 years ago by mattgalbraith
  2

• try to override show function without redefining a new class

  #24 opened 3 years ago by stemangiola
  0

• as_tibble() and slice_sample() cannot handle a column named $cell

  #38 opened 3 years ago by ttriche
  4

• Beta testing - do you know somebody?

  #3 opened 3 years ago by stemangiola
  2

• update github action

  #16 opened 4 years ago by stemangiola
  1

• comply to Bioconductor review

  #8 opened 4 years ago by stemangiola
  14