Recent Releases of tidybulk
tidybulk - Prepare for the next Bioc release
What's Changed
- Enhance entrezoverto_gsea function by adding msigdbr version check,… by @stemangiola in https://github.com/stemangiola/tidybulk/pull/322
- fix gene enrichment internal arguments by @stemangiola in https://github.com/stemangiola/tidybulk/pull/323
- take care of matrix conversion by @stemangiola in https://github.com/stemangiola/tidybulk/pull/321
- Resolve confounders without altering original columns by @stemangiola in https://github.com/stemangiola/tidybulk/pull/324
- fix docs by @stemangiola in https://github.com/stemangiola/tidybulk/pull/325
Full Changelog: https://github.com/stemangiola/tidybulk/compare/v1.17.9...v1.19.1
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Published by stemangiola 11 months ago
tidybulk - Feb 2025
What's Changed
- if SummarizedExperiment is empty, do not fail by @stemangiola in https://github.com/stemangiola/tidybulk/pull/291
- fixes by @stemangiola in https://github.com/stemangiola/tidybulk/pull/293
- add method glmmTMB by @stemangiola in https://github.com/stemangiola/tidybulk/pull/296
- use Matrix library for sparse counts by @stemangiola in https://github.com/stemangiola/tidybulk/pull/294
- drop sample argument by @stemangiola in https://github.com/stemangiola/tidybulk/pull/300
- Fix bug reduce dimension by @stemangiola in https://github.com/stemangiola/tidybulk/pull/299
- De no forking by @stemangiola in https://github.com/stemangiola/tidybulk/pull/303
- Improve random effect dispersion by @stemangiola in https://github.com/stemangiola/tidybulk/pull/305
- Improve glmmseq by @stemangiola in https://github.com/stemangiola/tidybulk/pull/306
- Fix bioc error by @stemangiola in https://github.com/stemangiola/tidybulk/pull/310
- Fix interactions for de by @stemangiola in https://github.com/stemangiola/tidybulk/pull/311
- replace everywhere one_of by @stemangiola in https://github.com/stemangiola/tidybulk/pull/312
- Quantile normalise custom target by @stemangiola in https://github.com/stemangiola/tidybulk/pull/313
- return tibble with get action by @stemangiola in https://github.com/stemangiola/tidybulk/pull/314
- add method by @stemangiola in https://github.com/stemangiola/tidybulk/pull/307
- use matrix multiplication by @stemangiola in https://github.com/stemangiola/tidybulk/pull/315
- use a function to drop env by @stemangiola in https://github.com/stemangiola/tidybulk/pull/319
- Update confounders and filtering by @stemangiola in https://github.com/stemangiola/tidybulk/pull/318
Full Changelog: https://github.com/stemangiola/tidybulk/compare/v1.11.7...v1.17.9
- R
Published by stemangiola about 1 year ago
tidybulk - v1.11.7
What's Changed
- drop dataset by @stemangiola in https://github.com/stemangiola/tidybulk/pull/289
- Custom dispersion de by @stemangiola in https://github.com/stemangiola/tidybulk/pull/288
- Add fast quantile normalisation based on target sample, for 1000+ sample dataset. Add preprocess core method by @stemangiola in https://github.com/stemangiola/tidybulk/pull/290
Full Changelog: https://github.com/stemangiola/tidybulk/compare/v1.11.6...v1.11.7
- R
Published by stemangiola over 2 years ago
tidybulk - v1.11.6
What's Changed
- Add combat seq by @stemangiola in https://github.com/stemangiola/tidybulk/pull/281
- modify test to allow tidy mutate by @stemangiola in https://github.com/stemangiola/tidybulk/pull/284
- Dev by @stemangiola in https://github.com/stemangiola/tidybulk/pull/283
Full Changelog: https://github.com/stemangiola/tidybulk/compare/v1.11.5...v1.11.6
- R
Published by stemangiola over 2 years ago
tidybulk - v1.11.5 - random effect differential abundance and more
What's Changed
- Drop bind generics by @stemangiola in https://github.com/stemangiola/tidybulk/pull/271
- Allow custom assay for se de by @stemangiola in https://github.com/stemangiola/tidybulk/pull/274
- add tibble-based method by @stemangiola in https://github.com/stemangiola/tidybulk/pull/276
- added quantile normalisation by @stemangiola in https://github.com/stemangiola/tidybulk/pull/277
- Solve lme4 memory issue by @stemangiola in https://github.com/stemangiola/tidybulk/pull/278
- Identify abundant robustify by @stemangiola in https://github.com/stemangiola/tidybulk/pull/279
- Dev by @stemangiola in https://github.com/stemangiola/tidybulk/pull/275
Full Changelog: https://github.com/stemangiola/tidybulk/compare/v1.11.3...v1.11.5
- R
Published by stemangiola over 2 years ago
tidybulk - Release update for RMedicine2023
What's Changed
- Update introduction.Rmd by @stemangiola in https://github.com/stemangiola/tidybulk/pull/267
- Add LFC threshold tests for DESeq2 by @mikelove in https://github.com/stemangiola/tidybulk/pull/268
New Contributors
- @mikelove made their first contribution in https://github.com/stemangiola/tidybulk/pull/268
Full Changelog: https://github.com/stemangiola/tidybulk/compare/v1.11.1...v1.11.3
- R
Published by stemangiola over 2 years ago
tidybulk - DEVELOPMENT_3_17
What's Changed
- fixes by @stemangiola in https://github.com/stemangiola/tidybulk/pull/250
- Fix image2 by @mblue9 in https://github.com/stemangiola/tidybulk/pull/254
- change message frequency by @stemangiola in https://github.com/stemangiola/tidybulk/pull/255
- Dev by @stemangiola in https://github.com/stemangiola/tidybulk/pull/252
- Stemangiola patch 1 by @stemangiola in https://github.com/stemangiola/tidybulk/pull/257
- Release 3 15 by @stemangiola in https://github.com/stemangiola/tidybulk/pull/256
- Improve deconv docs by @stemangiola in https://github.com/stemangiola/tidybulk/pull/258
- Update check-bioc.yml by @mblue9 in https://github.com/stemangiola/tidybulk/pull/260
- add messaging by @stemangiola in https://github.com/stemangiola/tidybulk/pull/262
Full Changelog: https://github.com/stemangiola/tidybulk/compare/v1.9.2...v1.11.1
- R
Published by stemangiola about 3 years ago
tidybulk - Release for BioC2022
Changes in version 1.9.2, Bioconductor 3.16 Dev
- Improve aggregate_duplicates for tibble and SummarizedExperiment
- Fix epic deconvolution when using DelayedMatrix
- Allow as_SummarizedExperiment with multiple columns identifiers for .sample and .feature
What's Changed
- error if there are NAs in the .transcript column by @stemangiola in https://github.com/stemangiola/tidybulk/pull/248
- convert DelayedMatrix and fixed sample column name by @stemangiola in https://github.com/stemangiola/tidybulk/pull/247
- as_SE with multiple columns as input by @stemangiola in https://github.com/stemangiola/tidybulk/pull/249
- improve docs for deconvolution by @stemangiola in https://github.com/stemangiola/tidybulk/pull/246
Full Changelog: https://github.com/stemangiola/tidybulk/compare/v1.7.4...v1.9.2
- R
Published by stemangiola over 3 years ago
tidybulk - Dev Bioconductor 3.16
What's Changed
- Sparse counts by @stemangiola in https://github.com/stemangiola/tidybulk/pull/211
- Cibersort check 0 counts by @stemangiola in https://github.com/stemangiola/tidybulk/pull/217
- Update NEWS.rd by @mblue9 in https://github.com/stemangiola/tidybulk/pull/220
- Fix typo in DESeq raw result variable return by @antass in https://github.com/stemangiola/tidybulk/pull/223
- print message if reference is not defined by the user by @stemangiola in https://github.com/stemangiola/tidybulk/pull/226
- Cibersort check 0 counts by @stemangiola in https://github.com/stemangiola/tidybulk/pull/218
- Sparse counts by @stemangiola in https://github.com/stemangiola/tidybulk/pull/207
- Dev by @stemangiola in https://github.com/stemangiola/tidybulk/pull/227
- try fix by @stemangiola in https://github.com/stemangiola/tidybulk/pull/228
- Update actions to Bioc 3.14 by @mblue9 in https://github.com/stemangiola/tidybulk/pull/229
- For jian by @stemangiola in https://github.com/stemangiola/tidybulk/pull/230
- Dev by @stemangiola in https://github.com/stemangiola/tidybulk/pull/231
- add argument for scaling if not scaled by @stemangiola in https://github.com/stemangiola/tidybulk/pull/232
- Dev by @stemangiola in https://github.com/stemangiola/tidybulk/pull/233
- Update github action to Bioc 3.15 by @mblue9 in https://github.com/stemangiola/tidybulk/pull/234
- implement new vocabulary by @stemangiola in https://github.com/stemangiola/tidybulk/pull/237
- deprecate .contrasts and update tests by @stemangiola in https://github.com/stemangiola/tidybulk/pull/239
- avoid human annotation by @stemangiola in https://github.com/stemangiola/tidybulk/pull/238
- allow other feature column for SE by @stemangiola in https://github.com/stemangiola/tidybulk/pull/236
- Polish aggregation tibble by @stemangiola in https://github.com/stemangiola/tidybulk/pull/235
- implementation parallel cibersort by @stemangiola in https://github.com/stemangiola/tidybulk/pull/244
- deprecation untested by @stemangiola in https://github.com/stemangiola/tidybulk/pull/241
- Dev by @stemangiola in https://github.com/stemangiola/tidybulk/pull/242
New Contributors
- @antass made their first contribution in https://github.com/stemangiola/tidybulk/pull/223
Full Changelog: https://github.com/stemangiola/tidybulk/compare/v1.5.5...v1.7.4
- R
Published by stemangiola over 3 years ago
tidybulk - Genome Biology accepted article
This is the version was used to build the Genome Biology article "tidybulk: an R tidy framework for modular transcriptomic data analysis"
- R
Published by stemangiola about 5 years ago
tidybulk - Genome Biology - Rebuttal 1
This is the release with which we submitted the first rebuttal to Genome Biology
- R
Published by stemangiola over 5 years ago