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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| library(scuttle) | ||
| library(celldex) | ||
| library(SingleR) | ||
| library(BiocParallel) | ||
| library(HCAquery) | ||
| library(SingleCellExperiment) | ||
| library(tidySingleCellExperiment) | ||
| library(digest) | ||
| library(openssl) | ||
| library(stringr) | ||
| library(HDF5Array) | ||
| monocyte_reference = celldex::MonacoImmuneData() | ||
|
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||
|
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||
| readRDS("/vast/projects/RCP/human_cell_atlas/metadata.rds") |> | ||
| filter(.cell %in% ( | ||
| readRDS("dev/curated_annotation.rds") |> | ||
| filter(cell_type_harmonised=="cd4 t") |> | ||
| pull(.cell) | ||
| )) |> | ||
| unite("file_id_db", c(file_id, cell_type), remove = FALSE) |> | ||
| mutate(file_id_db = file_id_db |> md5() |> as.character()) |> | ||
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|
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| get_SingleCellExperiment("/vast/projects/RCP/human_cell_atlas/splitted_DB2_data") |> | ||
|
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||
| # Annotate | ||
| logNormCounts(assay.type = "X") |> | ||
| SingleR( | ||
| ref = monocyte_reference, | ||
| assay.type.test=1, | ||
| labels = monocyte_reference$label.fine | ||
| ) |> | ||
| saveRDS("reannotate_cd4.rds") |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| library(scuttle) | ||
| library(celldex) | ||
| library(SingleR) | ||
| library(BiocParallel) | ||
| library(HCAquery) | ||
| library(SingleCellExperiment) | ||
| library(tidySingleCellExperiment) | ||
| library(digest) | ||
| library(openssl) | ||
| library(stringr) | ||
| library(HDF5Array) | ||
| monocyte_reference =celldex::MonacoImmuneData() | ||
|
|
||
|
|
||
| readRDS("/vast/projects/RCP/human_cell_atlas/metadata.rds") |> | ||
| filter(.cell %in% ( | ||
| readRDS("dev/curated_annotation.rds") |> | ||
| filter(cell_type_harmonised=="cd8 t") |> | ||
| pull(.cell) | ||
| )) |> | ||
| unite("file_id_db", c(file_id, cell_type), remove = FALSE) |> | ||
| mutate(file_id_db = file_id_db |> md5() |> as.character()) |> | ||
|
|
||
| get_SingleCellExperiment("/vast/projects/RCP/human_cell_atlas/splitted_DB2_data") |> | ||
|
|
||
| # Annotate | ||
| logNormCounts(assay.type = "X") |> | ||
|
|
||
| SingleR( | ||
| ref = monocyte_reference, | ||
| assay.type.test=1, | ||
| labels = monocyte_reference$label.fine | ||
| ) |> | ||
| saveRDS("reannotate_cd8.rds") |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| library(scuttle) | ||
| library(celldex) | ||
| library(SingleR) | ||
| library(BiocParallel) | ||
| library(HCAquery) | ||
| library(SingleCellExperiment) | ||
| library(tidySingleCellExperiment) | ||
| library(digest) | ||
| library(openssl) | ||
| library(stringr) | ||
| library(HDF5Array) | ||
| monocyte_reference =celldex::MonacoImmuneData() | ||
|
|
||
|
|
||
|
|
||
| readRDS("/vast/projects/RCP/human_cell_atlas/metadata.rds") |> | ||
| filter(.cell %in% ( | ||
| readRDS("dev/curated_annotation.rds") |> | ||
| filter(cell_type_harmonised=="monocytes") |> | ||
| pull(.cell) | ||
| )) |> | ||
| unite("file_id_db", c(file_id, cell_type), remove = FALSE) |> | ||
| mutate(file_id_db = file_id_db |> md5() |> as.character()) |> | ||
|
|
||
| get_SingleCellExperiment("/vast/projects/RCP/human_cell_atlas/splitted_DB2_data") |> | ||
|
|
||
| # Annotate | ||
| logNormCounts(assay.type = "X") |> | ||
| SingleR( | ||
| ref = monocyte_reference, | ||
| assay.type.test=1, | ||
| labels = monocyte_reference$label.fine | ||
| ) |> | ||
| saveRDS("reannotate_monocytes.rds") |