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tidyomics

6 indexed repositories · View on GitHub

tidybulk
Brings bulk and pseudobulk transcriptomics to the tidyverse

R · 182 stars
plyranges
A grammar of genomic data transformation

R · 156 stars
tidySingleCellExperiment
Brings SingleCellExperiment objects to the tidyverse

R · 36 stars
tidySummarizedExperiment
Brings SummarizedExperiment to the tidyverse

R · 31 stars
tidyprint
Centralised biological data tidy abstractions and messaging

R · 2 stars
omicslog
Log operations of R omic analyses

R · 2 stars

Beginner friendly Everything

Open All

slice_sample() can't use width Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

tidyomics/plyranges#130 · Opened Sep 9, 2026
`filter()` cannot access colData columns with non-syntactic names Open

tidyomics/tidySummarizedExperiment#124 · 1 comment · 2 reactions · 2 assignees · Opened Aug 17, 2026
Feature request - hash recording Open

tidyomics/omicslog#13 · 1 assignee · Opened May 21, 2026
plyranges v1.28.0 throws error if the name and score column has NA Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

tidyomics/plyranges#125 · 1 comment · Opened Apr 5, 2026
describe_transcript() returns all NA for description (example from documentation) Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

tidyomics/tidybulk#339 · Opened Mar 26, 2026
character string is not in a standard unambiguous format Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

tidyomics/tidyprint#32 · Opened Mar 18, 2026
`bind_ranges` operating on a GRangesList Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

tidyomics/plyranges#118 · Opened Feb 25, 2026
proof-of-concept for anndata implementation Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

tidyomics/omicslog#10 · 13 comments · Opened Jan 6, 2026
Feature-request Open

tidyomics/omicslog#9 · 3 comments · 2 reactions · 1 assignee · Opened Jan 6, 2026
if a SE has 0 rows we have error Open

tidyomics/tidyprint#30 · 1 assignee · Opened Dec 16, 2025
feature request: Aggregate by a variable in rowData or colData Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

tidyomics/tidySummarizedExperiment#115 · 1 reaction · Opened Dec 4, 2025
GRN functionalities for tidybulk2 Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

tidyomics/tidybulk#334 · 2 comments · 1 reaction · Opened Oct 28, 2025
for `SCE` Add conditional print method for objects that contain alternative experiments Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

tidyomics/tidyprint#26 · Opened Oct 25, 2025
for `tidySCE` mark view only column Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

tidyomics/tidyprint#24 · Opened Oct 25, 2025
Extending log information when exporting to a file Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

tidyomics/omicslog#3 · 3 comments · Opened Jun 3, 2025
Option to create conda or docker file Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

tidyomics/omicslog#2 · Opened Jun 3, 2025
Discrepancy in DE results from base DESeq2 and tidybulk DESeq2 method Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

tidyomics/tidybulk#328 · 8 comments · Opened May 12, 2025
add reference to each exported function Open

tidyomics/tidySingleCellExperiment#114 · 1 reaction · 1 assignee · Opened Mar 7, 2025
Add example on vignettes and README of how to check for dispersion, and MA plot after DE for egdeR/limma/DESeq2 Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

tidyomics/tidybulk#320 · Opened Dec 18, 2024
add check for duplicated rows for `aggregate_cells` Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

tidyomics/tidySingleCellExperiment#111 · Opened Sep 16, 2024
The sample data of the `test_gene_enrichment()` function reports an error and cannot be used. Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

tidyomics/tidybulk#316 · 2 comments · 1 reaction · Opened Jul 25, 2024
aggregate_cells takes too long Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

tidyomics/tidySingleCellExperiment#110 · 3 comments · Opened Jun 27, 2024
Path of images of stemangiola.github.io/tidySingleCellExperimen not correct Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

tidyomics/tidySingleCellExperiment#109 · Opened Jun 18, 2024
[feature request] use cli printing Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

tidyomics/tidySingleCellExperiment#108 · Opened May 30, 2024
feature request: join_features shape="long" should carry the rowData as well, similarly to `tidySummarizedExperiment` Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

tidyomics/tidySingleCellExperiment#107 · Opened May 21, 2024
[FEATURE REQUEST] mutate(across()) ? Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

tidyomics/plyranges#110 · Opened Apr 10, 2024
[BUG] Inconsistent behaviour of join_nearest_downstream() with one unstranded range set? Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

tidyomics/plyranges#106 · 1 comment · Opened Dec 5, 2023
Add the method to simplify complete confounders is they are not factor of interest Open

enhancement

tidyomics/tidybulk#301 · 1 assignee · Opened Nov 15, 2023
Warning in package check: checking S3 generic/method consistency for `group_*` Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

tidyomics/plyranges#104 · Opened Nov 12, 2023
Prepare for upcoming Seurat v5 release Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

tidyomics/tidybulk#298 · Opened Oct 3, 2023
the attribute "internals" $ tt_columns abundance_scaled, carries the environment with it inflating the RDS file size Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

tidyomics/tidybulk#295 · Opened Sep 11, 2023
Clarifications about `.abundance_counts` Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

tidyomics/tidySingleCellExperiment#95 · 4 comments · Opened Sep 8, 2023
`tidySCE`: `slice` masks tidyverse::slice Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

tidyomics/tidySingleCellExperiment#88 · Opened Aug 24, 2023
`tidySCE` deal with missing assay names Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

tidyomics/tidySingleCellExperiment#82 · Opened Aug 21, 2023
`tidySCE` Functionality to see and access the altExp slot Open

enhancement

tidyomics/tidySingleCellExperiment#81 · 22 comments · 1 assignee · Opened Aug 16, 2023
Tidy operations with `tidySE` when `colData` and `rowData` share column names Open

bug

tidyomics/tidySummarizedExperiment#76 · 6 comments · 1 assignee · Opened Jul 21, 2023
Implement `group_by` and `with_groups` for `tidySummarizedExperiment` Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 15/100

tidyomics/tidySummarizedExperiment#75 · 1 comment · Opened Jul 20, 2023
Implement `group_by` and `with_groups` for `tidySingleCellExperiment` and `tidyseurat` Open

enhancement

tidyomics/tidySingleCellExperiment#71 · 16 comments · 1 assignee · Opened Jul 20, 2023
Speed up `nest` and `unnest` for massive datasets in `tidySingleCellExperiment` Open

enhancement

tidyomics/tidySingleCellExperiment#70 · 4 comments · 1 assignee · Opened Jul 19, 2023
Warning in CHECK, mistery Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

tidyomics/tidybulk#273 · Opened Jun 29, 2023
speed up as_tibble in case I have nested columns in the metadata e.g. TCR Open

bug enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

tidyomics/tidySingleCellExperiment#66 · 3 comments · Opened Jun 19, 2023
Bug when using `joinFeatures` + `SingleCellExperiment` with 1 cell Open

tidyomics/tidySingleCellExperiment#60 · 1 comment · 1 assignee · Opened Apr 20, 2023
NSBS object error when trying to filter by overlap GRanges object from read_bam() Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

tidyomics/plyranges#102 · Opened Apr 2, 2023
[BUG] reduce_ranges silently creates list columns and fails to do so so if nothing is reduced Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

tidyomics/plyranges#101 · Opened Mar 1, 2023
subsample sce object based on factor in colData Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

tidyomics/tidySingleCellExperiment#56 · 1 comment · Opened Feb 19, 2023
flip_strand() function? Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

tidyomics/plyranges#100 · 1 comment · Opened Feb 14, 2023
pathway analysis using tidybulk Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

tidyomics/tidybulk#263 · 8 comments · Opened Jan 13, 2023
Selecting nonexistent columns prints confusing error message Open

Difficulty 2/5 1-3 hours Newbie friendliness 62/100

tidyomics/plyranges#99 · 2 reactions · Opened Jan 10, 2023
If only one assay is present and is nameless, the assay column is not printed Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

tidyomics/tidyprint#25 · 2 comments · Opened May 26, 2022
[feature request] add .drop argument to group_by, e.g. to include empty seqlevels Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

tidyomics/plyranges#95 · Opened Feb 24, 2022

tidyomics

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