Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Get pseudobulk api #137

Merged
merged 25 commits into from
May 20, 2024
Merged

Get pseudobulk api #137

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
25 commits
Select commit Hold shift + click to select a range
5870fa4
create pseudobulk api
myushen Apr 16, 2024
1f6bf91
dontrun get_pseudobulk API examples in the function documentation
myushen Apr 16, 2024
d86f7df
create param_validation function which serves both get_pseudobulk and…
myushen Apr 18, 2024
f46587b
link pseudobulk to cloud
myushen Apr 24, 2024
95fe0e4
fix an testthat example issue
myushen Apr 24, 2024
306945c
Squashed commit of the following:
myushen May 1, 2024
a7e2987
unify functions
myushen May 1, 2024
d10ef14
Merge branch 'master' into get-pseudobulk-api
myushen May 1, 2024
93143cd
fix a test-query issue in github actions
myushen May 1, 2024
e3d4937
Merge branch 'get-pseudobulk-api' of https://github.com/myushen/Curat…
myushen May 1, 2024
095a051
try again
myushen May 1, 2024
88f0078
try again test-query
myushen May 2, 2024
8c0b8dc
adapt metadata sample-level columns to pseudobulk
myushen May 3, 2024
84e6f94
allow selected gene names in pseudobulk
myushen May 6, 2024
3f82de0
Squashed commit of the following:
myushen May 6, 2024
38d655d
rename normalisation tech name for pseudobulk. remove API test-query …
myushen May 8, 2024
c9790c9
Merge branch 'get-pseudobulk-api-debug' into get-pseudobulk-api
myushen May 13, 2024
58351f3
add get_pseudobulk test query
myushen May 16, 2024
c0a4049
Merge branch 'get-pseudobulk-api-debug' into get-pseudobulk-api
myushen May 16, 2024
7708579
fix assay name
myushen May 16, 2024
70ddc73
Merge branch 'get-pseudobulk-api-debug' of github.com:myushen/Curated…
myushen May 17, 2024
5b83919
Merge branch 'get-pseudobulk-api-debug' into get-pseudobulk-api
myushen May 17, 2024
cb6ba29
update version for two APIs and one minor bug
myushen May 20, 2024
10458a9
Merge branch 'get-pseudobulk-api-debug' into get-pseudobulk-api
myushen May 20, 2024
e1fdcab
Add stringfish as a runtime dependency
multimeric May 20, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 3 additions & 2 deletions DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Type: Package
Package: CuratedAtlasQueryR
Title: Queries the Human Cell Atlas
Version: 1.1.3
Version: 1.3.4
Authors@R: c(
person(
"Stefano",
Expand Down Expand Up @@ -94,7 +94,8 @@ Imports:
dbplyr (>= 2.3.0),
duckdb,
stringr,
checkmate
checkmate,
stringfish
Suggests:
zellkonverter,
rmarkdown,
Expand Down
4 changes: 1 addition & 3 deletions NAMESPACE
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,14 @@ export(get_SingleCellExperiment)
export(get_database_url)
export(get_default_cache_dir)
export(get_metadata)
export(get_pseudobulk)
export(get_seurat)
export(get_single_cell_experiment)
export(get_unharmonised_metadata)
export(import_metadata_counts)
importFrom(BiocGenerics,cbind)
importFrom(DBI,dbConnect)
importFrom(DBI,dbDisconnect)
importFrom(HDF5Array,HDF5RealizationSink)
importFrom(HDF5Array,loadHDF5SummarizedExperiment)
importFrom(HDF5Array,saveHDF5SummarizedExperiment)
importFrom(S4Vectors,"metadata<-")
Expand All @@ -24,7 +24,6 @@ importFrom(SeuratObject,as.Seurat)
importFrom(SeuratObject,as.sparse)
importFrom(SingleCellExperiment,"reducedDims<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,combineCols)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SingleCellExperiment,rowData)
importFrom(SummarizedExperiment,"assayNames<-")
Expand Down Expand Up @@ -80,7 +79,6 @@ importFrom(purrr,reduce)
importFrom(purrr,set_names)
importFrom(purrr,walk)
importFrom(rlang,.data)
importFrom(stats,setNames)
importFrom(stringr,str_detect)
importFrom(stringr,str_remove_all)
importFrom(stringr,str_replace_all)
Expand Down
Loading
Loading