Authors
diff --git a/docs/index.html b/docs/index.html index bfd8d00ef..a2713da36 100644 --- a/docs/index.html +++ b/docs/index.html @@ -32,7 +32,7 @@ @@ -81,36 +81,36 @@
R method
-if (!requireNamespace("remotes", quietly = TRUE)) {
- install.packages("remotes")
-}
-Sys.setenv(R_REMOTES_UPGRADE = "always")
-# Set `GITHUB_PAT` in `~/.Renviron` if you get a rate limit error.
-remotes::install_github("hbc/bcbioRNASingleCell")
+if (!requireNamespace("remotes", quietly = TRUE)) {
+ install.packages("remotes")
+}
+Sys.setenv(R_REMOTES_UPGRADE = "always")
+# Set `GITHUB_PAT` in `~/.Renviron` if you get a rate limit error.
+remotes::install_github("hbc/bcbioSingleCell")
Here’s how to update to the latest version on GitHub:
-
+Sys.setenv(R_REMOTES_UPGRADE = "always")
+remotes::update_packages()
Always check that your Bioconductor installation is valid before proceeding.
-if (!requireNamespace("BiocManager", quietly = TRUE)) {
- install.packages("BiocManager")
-}
-BiocManager::valid()
+if (!requireNamespace("BiocManager", quietly = TRUE)) {
+ install.packages("BiocManager")
+}
+BiocManager::valid()
Load bcbio single-cell RNA-seq data
-library(bcbioSingleCell)
-bcb <- bcbioSingleCell(
- uploadDir = "indrops/final",
- interestingGroups = c("genotype", "treatment"),
- sampleMetadataFile = "sample_metadata.csv",
- organism = "Homo sapiens",
- ensemblRelease = 90L
-)
-saveData(bcb, dir = ".")
+library(bcbioSingleCell)
+bcb <- bcbioSingleCell(
+ uploadDir = "indrops/final",
+ interestingGroups = c("genotype", "treatment"),
+ sampleMetadataFile = "sample_metadata.csv",
+ organism = "Homo sapiens",
+ ensemblRelease = 90L
+)
+saveData(bcb, dir = ".")
This will return a bcbioSingleCell object, which is an extension of the Bioconductor SingleCellExperiment container class. Consult the bcbioSingleCell() constructor function documentation for detailed information on the supported parameters:
-
+help(topic = "bcbioSingleCell", package = "bcbioSingleCell")
@@ -123,77 +123,77 @@
Consult the bcbio documentation for more information on how to configure an inDrops run prior to loading into R with the bcbioSingleCell() function.
-description
-index
-sequence
-sampleName
-aggregate
-genotype
+description
+index
+sequence
+sampleName
+aggregate
+genotype
-indrops1
-1
-CTCTCTAT
-sample1_1
-sample1
-wildtype
+indrops1
+1
+CTCTCTAT
+sample1_1
+sample1
+wildtype
-indrops1
-2
-TATCCTCT
-sample2_1
-sample2
-knockout
+indrops1
+2
+TATCCTCT
+sample2_1
+sample2
+knockout
-indrops1
-3
-GTAAGGAG
-sample3_1
-sample3
-wildtype
+indrops1
+3
+GTAAGGAG
+sample3_1
+sample3
+wildtype
-indrops1
-4
-ACTGCATA
-sample4_1
-sample4
-knockout
+indrops1
+4
+ACTGCATA
+sample4_1
+sample4
+knockout
-indrops2
-1
-CTCTCTAT
-sample1_2
-sample1
-wildtype
+indrops2
+1
+CTCTCTAT
+sample1_2
+sample1
+wildtype
-indrops2
-2
-TATCCTCT
-sample1_2
-sample2
-knockout
+indrops2
+2
+TATCCTCT
+sample1_2
+sample2
+knockout
-indrops2
-3
-GTAAGGAG
-sample1_2
-sample3
-wildtype
+indrops2
+3
+GTAAGGAG
+sample1_2
+sample3
+wildtype
-indrops2
-4
-ACTGCATA
-sample1_2
-sample4
-knockout
+indrops2
+4
+ACTGCATA
+sample1_2
+sample4
+knockout
@@ -205,25 +205,25 @@
This is our current method for handling 10X Genomics Chromium and Illumina SureCell cell barcodes.
-description
-genotype
+description
+genotype
-sample1
-wildtype
+sample1
+wildtype
-sample2
-knockout
+sample2
+knockout
-sample3
-wildtype
+sample3
+wildtype
-sample4
-knockout
+sample4
+knockout
@@ -232,9 +232,9 @@
Invalid object
If you encounter a validObject error when attempting to load a bcbioSingleCell object from a previous analysis, run this step to update the object to the current version of the package:
-
+object <- updateObject(object)
+validObject(object)
+## [1] TRUE
@@ -304,7 +304,7 @@ Dev status
diff --git a/docs/news/index.html b/docs/news/index.html
index 02af27e48..63989cd93 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -8,11 +8,13 @@
News • bcbioSingleCell
+
+
@@ -34,10 +36,12 @@
+
+
@@ -65,7 +69,7 @@
@@ -84,7 +88,6 @@
Changelog
R method
-if (!requireNamespace("remotes", quietly = TRUE)) {
- install.packages("remotes")
-}
-Sys.setenv(R_REMOTES_UPGRADE = "always")
-# Set `GITHUB_PAT` in `~/.Renviron` if you get a rate limit error.
-remotes::install_github("hbc/bcbioRNASingleCell")if (!requireNamespace("remotes", quietly = TRUE)) {
+ install.packages("remotes")
+}
+Sys.setenv(R_REMOTES_UPGRADE = "always")
+# Set `GITHUB_PAT` in `~/.Renviron` if you get a rate limit error.
+remotes::install_github("hbc/bcbioSingleCell")Here’s how to update to the latest version on GitHub:
- +Sys.setenv(R_REMOTES_UPGRADE = "always")
+remotes::update_packages()Always check that your Bioconductor installation is valid before proceeding.
-if (!requireNamespace("BiocManager", quietly = TRUE)) {
- install.packages("BiocManager")
-}
-BiocManager::valid()if (!requireNamespace("BiocManager", quietly = TRUE)) {
+ install.packages("BiocManager")
+}
+BiocManager::valid()Load bcbio single-cell RNA-seq data
-library(bcbioSingleCell)
-bcb <- bcbioSingleCell(
- uploadDir = "indrops/final",
- interestingGroups = c("genotype", "treatment"),
- sampleMetadataFile = "sample_metadata.csv",
- organism = "Homo sapiens",
- ensemblRelease = 90L
-)
-saveData(bcb, dir = ".")library(bcbioSingleCell)
+bcb <- bcbioSingleCell(
+ uploadDir = "indrops/final",
+ interestingGroups = c("genotype", "treatment"),
+ sampleMetadataFile = "sample_metadata.csv",
+ organism = "Homo sapiens",
+ ensemblRelease = 90L
+)
+saveData(bcb, dir = ".")This will return a bcbioSingleCell object, which is an extension of the Bioconductor SingleCellExperiment container class. Consult the bcbioSingleCell() constructor function documentation for detailed information on the supported parameters:
help(topic = "bcbioSingleCell", package = "bcbioSingleCell")
@@ -123,77 +123,77 @@
Consult the bcbio documentation for more information on how to configure an inDrops run prior to loading into R with the bcbioSingleCell() function.
| description | -index | -sequence | -sampleName | -aggregate | -genotype | +description | +index | +sequence | +sampleName | +aggregate | +genotype |
|---|---|---|---|---|---|---|---|---|---|---|---|
| indrops1 | -1 | -CTCTCTAT | -sample1_1 | -sample1 | -wildtype | +indrops1 | +1 | +CTCTCTAT | +sample1_1 | +sample1 | +wildtype |
| indrops1 | -2 | -TATCCTCT | -sample2_1 | -sample2 | -knockout | +indrops1 | +2 | +TATCCTCT | +sample2_1 | +sample2 | +knockout |
| indrops1 | -3 | -GTAAGGAG | -sample3_1 | -sample3 | -wildtype | +indrops1 | +3 | +GTAAGGAG | +sample3_1 | +sample3 | +wildtype |
| indrops1 | -4 | -ACTGCATA | -sample4_1 | -sample4 | -knockout | +indrops1 | +4 | +ACTGCATA | +sample4_1 | +sample4 | +knockout |
| indrops2 | -1 | -CTCTCTAT | -sample1_2 | -sample1 | -wildtype | +indrops2 | +1 | +CTCTCTAT | +sample1_2 | +sample1 | +wildtype |
| indrops2 | -2 | -TATCCTCT | -sample1_2 | -sample2 | -knockout | +indrops2 | +2 | +TATCCTCT | +sample1_2 | +sample2 | +knockout |
| indrops2 | -3 | -GTAAGGAG | -sample1_2 | -sample3 | -wildtype | +indrops2 | +3 | +GTAAGGAG | +sample1_2 | +sample3 | +wildtype |
| indrops2 | -4 | -ACTGCATA | -sample1_2 | -sample4 | -knockout | +indrops2 | +4 | +ACTGCATA | +sample1_2 | +sample4 | +knockout |
This is our current method for handling 10X Genomics Chromium and Illumina SureCell cell barcodes.
| description | -genotype | +description | +genotype |
|---|---|---|---|
| sample1 | -wildtype | +sample1 | +wildtype |
| sample2 | -knockout | +sample2 | +knockout |
| sample3 | -wildtype | +sample3 | +wildtype |
| sample4 | -knockout | +sample4 | +knockout |
Invalid object
If you encounter a validObject error when attempting to load a bcbioSingleCell object from a previous analysis, run this step to update the object to the current version of the package:
object <- updateObject(object)
+validObject(object)
+## [1] TRUE
