stemangiola/tidybulk issues and pull requests

#314 - return tibble with get action

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

#313 - Quantile normalise custom target

Pull Request - State: closed - Opened by stemangiola 2 months ago

#312 - replace everywhere one_of

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

#311 - Fix interactions for de

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

#310 - Fix bioc error

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

#309 - limma:MakeContrasts integration issues

Issue - State: closed - Opened by aodainic7 5 months ago - 2 comments
Labels: bug

#308 - Improve documentation and package imports

Pull Request - State: open - Opened by william-hutchison 6 months ago - 22 comments

#307 - add method

Pull Request - State: closed - Opened by stemangiola 7 months ago

#306 - Improve glmmseq

Pull Request - State: closed - Opened by stemangiola 7 months ago

#305 - Improve random effect dispersion

Pull Request - State: closed - Opened by stemangiola 7 months ago

#304 - use rworkflow

Pull Request - State: closed - Opened by stemangiola 7 months ago

#303 - De no forking

Pull Request - State: closed - Opened by stemangiola 8 months ago

#302 - changed github action

Pull Request - State: closed - Opened by stemangiola 8 months ago

#301 - Add the method to simplify complete confounders is they are not factor of interest

Issue - State: open - Opened by stemangiola 8 months ago
Labels: enhancement

#300 - drop sample argument

Pull Request - State: closed - Opened by stemangiola 8 months ago
Labels: bug

#299 - Fix bug reduce dimension

Pull Request - State: closed - Opened by stemangiola 8 months ago
Labels: bug

#298 - Prepare for upcoming Seurat v5 release

Issue - State: open - Opened by Gesmira 9 months ago

#297 - resolve tidyomics conflicts and docs clean up

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

#296 - add method glmmTMB

Pull Request - State: closed - Opened by stemangiola 10 months ago

#295 - the attribute "internals" $ tt_columns abundance_scaled, carries the environment with it inflating the RDS file size

Issue - State: open - Opened by stemangiola 10 months ago

#294 - use Matrix library for sparse counts

Pull Request - State: closed - Opened by stemangiola 10 months ago

#293 - fixes

Pull Request - State: closed - Opened by stemangiola 10 months ago

#292 - in `test_gene_rank` check if any feature is NA, because pivot_feature will fail

Issue - State: closed - Opened by stemangiola 10 months ago

#291 - if SummarizedExperiment is empty, do not fail

Pull Request - State: closed - Opened by stemangiola 10 months ago

#290 - add preprocess core method

Pull Request - State: closed - Opened by stemangiola 10 months ago

#289 - drop dataset

Pull Request - State: closed - Opened by stemangiola 10 months ago
Labels: bug

#288 - Custom dispersion de

Pull Request - State: closed - Opened by stemangiola 10 months ago - 1 comment

#287 - resolve conflicts for dplyr/tidyr funcs

Pull Request - State: closed - Opened by chilampoon 10 months ago - 15 comments

#286 - `tidybulk` Remove hard dependency for `DESeq2`

Issue - State: closed - Opened by stemangiola 11 months ago - 12 comments

#285 - turn pseudobulk from scRNAseq with logCPM value back to a seurat object with counts value?

Issue - State: closed - Opened by jiangzh-coder 12 months ago - 2 comments

#284 - modify test to allow tidy mutate

Pull Request - State: closed - Opened by stemangiola 12 months ago

#283 - Dev

Pull Request - State: closed - Opened by stemangiola 12 months ago

#282 - Improve the documentation for `tidybulk`

Issue - State: open - Opened by stemangiola 12 months ago - 29 comments
Labels: documentation, good first issue

#281 - Add combat seq

Pull Request - State: closed - Opened by stemangiola 12 months ago

#280 - test

Issue - State: closed - Opened by stemangiola 12 months ago

#279 - Identify abundant robustify

Pull Request - State: closed - Opened by stemangiola 12 months ago

#278 - Solve lme4 memory issue

Pull Request - State: closed - Opened by stemangiola 12 months ago

#277 - added quantile normalisation

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

#276 - add tibble based method

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

#275 - Dev

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

#274 - Allow custom assay for se de

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

#273 - Warning in CHECK, mistery

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

#272 - Solve conflicts tidyverse

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

#271 - Drop bind generics

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

#270 - Remove batch effect in test_differential_abundance

Issue - State: closed - Opened by jianwu1 about 1 year ago

#269 - The first element of assays in SE might be a matrix when using DESeq2 method

Pull Request - State: open - Opened by xiangpin about 1 year ago - 6 comments

#268 - Add LFC threshold tests for DESeq2

Pull Request - State: closed - Opened by mikelove over 1 year ago - 6 comments

#267 - Update introduction.Rmd

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

#266 - add ellipsis

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

#265 - Deprecate default de method

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

#264 - Design and contrasts for tidybulk test differential abundance function

Issue - State: closed - Opened by adityamahadevaniyer over 1 year ago - 9 comments

#263 - pathway analysis using tidybulk

Issue - State: open - Opened by adityamahadevaniyer over 1 year ago - 8 comments

#262 - add messaging

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

#261 - ERROR; return code from pthread_create() is 22

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

#260 - Update check-bioc.yml

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

#259 - github actions give preflight error for the whole tidy stack

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

#258 - Improve deconv docs

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

#257 - Stemangiola patch 1

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

#256 - Release 3 15

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

#255 - change message frequency

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

#254 - Fix image2

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

#253 - "Proportion of variance explained" values on reduce_dimensions() output

Issue - State: closed - Opened by canholyavkin almost 2 years ago - 1 comment

#252 - Dev

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

#251 - Fix image

Pull Request - State: closed - Opened by mblue9 almost 2 years ago - 3 comments

#250 - fixes

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