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stemangiola
/
tidybulk
Brings bulk and pseudobulk transcriptomics to the tidyverse
https://stemangiola.github.io/tidybulk/
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Add package installation messages
#317
william-hutchison
opened
2 weeks ago
0
The sample data of the `test_gene_enrichment()` function reports an error and cannot be used.
#316
zhangkaicr
opened
3 months ago
2
use matrix multiplication
#315
stemangiola
closed
1 month ago
0
return tibble with get action
#314
stemangiola
closed
5 months ago
0
Quantile normalise custom target
#313
stemangiola
closed
5 months ago
0
replace everywhere one_of
#312
stemangiola
closed
8 months ago
0
Fix interactions for de
#311
stemangiola
closed
9 months ago
0
Fix bioc error
#310
stemangiola
closed
9 months ago
0
limma:MakeContrasts integration issues
#309
aodainic7
closed
9 months ago
2
Improve documentation and package imports
#308
william-hutchison
opened
9 months ago
26
add method
#307
stemangiola
closed
3 months ago
0
Improve glmmseq
#306
stemangiola
closed
11 months ago
0
Improve random effect dispersion
#305
stemangiola
closed
11 months ago
0
use rworkflow
#304
stemangiola
closed
9 months ago
0
De no forking
#303
stemangiola
closed
11 months ago
0
changed github action
#302
stemangiola
closed
9 months ago
0
Add the method to simplify complete confounders is they are not factor of interest
#301
stemangiola
opened
11 months ago
0
drop sample argument
#300
stemangiola
closed
1 year ago
0
Fix bug reduce dimension
#299
stemangiola
closed
1 year ago
0
Prepare for upcoming Seurat v5 release
#298
Gesmira
opened
1 year ago
0
resolve tidyomics conflicts and docs clean up
#297
chilampoon
closed
1 year ago
12
add method glmmTMB
#296
stemangiola
closed
1 year ago
0
the attribute "internals" $ tt_columns abundance_scaled, carries the environment with it inflating the RDS file size
#295
stemangiola
opened
1 year ago
0
use Matrix library for sparse counts
#294
stemangiola
closed
1 year ago
0
fixes
#293
stemangiola
closed
1 year ago
0
in `test_gene_rank` check if any feature is NA, because pivot_feature will fail
#292
stemangiola
closed
1 year ago
0
if SummarizedExperiment is empty, do not fail
#291
stemangiola
closed
1 year ago
0
add preprocess core method
#290
stemangiola
closed
1 year ago
0
drop dataset
#289
stemangiola
closed
1 year ago
0
Custom dispersion de
#288
stemangiola
closed
1 year ago
1
resolve conflicts for dplyr/tidyr funcs
#287
chilampoon
closed
1 year ago
15
`tidybulk` Remove hard dependency for `DESeq2`
#286
stemangiola
closed
1 year ago
12
turn pseudobulk from scRNAseq with logCPM value back to a seurat object with counts value?
#285
jiangzh-coder
closed
1 year ago
2
modify test to allow tidy mutate
#284
stemangiola
closed
1 year ago
0
Dev
#283
stemangiola
closed
1 year ago
0
Improve the documentation for `tidybulk`
#282
stemangiola
opened
1 year ago
29
Add combat seq
#281
stemangiola
closed
1 year ago
0
test
#280
stemangiola
closed
1 year ago
0
Identify abundant robustify
#279
stemangiola
closed
1 year ago
0
Solve lme4 memory issue
#278
stemangiola
closed
1 year ago
0
added quantile normalisation
#277
stemangiola
closed
1 year ago
0
add tibble based method
#276
stemangiola
closed
1 year ago
0
Dev
#275
stemangiola
closed
1 year ago
0
Allow custom assay for se de
#274
stemangiola
closed
1 year ago
0
Warning in CHECK, mistery
#273
stemangiola
opened
1 year ago
0
Solve conflicts tidyverse
#272
stemangiola
closed
9 months ago
0
Drop bind generics
#271
stemangiola
closed
1 year ago
0
Remove batch effect in test_differential_abundance
#270
jianwu1
closed
1 year ago
0
The first element of assays in SE might be a matrix when using DESeq2 method
#269
xiangpin
opened
1 year ago
6
Add LFC threshold tests for DESeq2
#268
mikelove
closed
1 year ago
6
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