Files in campbio/scruff
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/alignRsubread.R
R/countUMI.R
R/data.R
R/demultiplex.R
R/global.R
R/gview.R
R/qcplots.R
R/rview.R
R/scruff.R
R/scruffFunctions.R
R/tenxBamqc.R
README.md
data-raw/10x/SRR5167880_E18_20160930_Neurons_Sample_01_filtered_barcode.R
data-raw/10x/barcodeCheck.R
data-raw/10x/cbWhitelist737KAugust2016.R
data-raw/Mus_musculus/GSE85755_CEL-Seq_barcodes_96.txt
data-raw/Mus_musculus/barcodeExample.R
data-raw/exampleFastqs.R
data-raw/figure/20180907_vdb_newplots_ercc_edit_Page_01.png
data-raw/figure/20180907_vdb_newplots_ercc_edit_Page_02.png
data-raw/figure/20180907_vdb_newplots_ercc_edit_Page_03.png
data-raw/figure/20180907_vdb_newplots_ercc_edit_Page_04.png
data-raw/figure/20180907_vdb_newplots_ercc_edit_Page_05.png
data-raw/figure/20180907_vdb_newplots_ercc_edit_Page_06.png
data-raw/figure/20180907_vdb_newplots_ercc_edit_Page_07.png
data-raw/figure/20180907_vdb_newplots_ercc_edit_Page_08.png
data-raw/figure/20180907_vdb_newplots_ercc_edit_Page_09.png
data-raw/figure/20180907_vdb_newplots_ercc_edit_Page_10.png
data-raw/figure/20180907_vdb_newplots_ercc_edit_Page_11.png
data-raw/figure/20180907_vdb_newplots_ercc_edit_Page_12.png
data-raw/figure/20180907_vdb_newplots_ercc_edit_Page_13.png
data-raw/figure/20181221_scruff_figure_4.png
data-raw/figure/20190124_scruff_figure_3.png
data-raw/figure/20190312_scruff_figure_5.png
data-raw/figure/20190312_scruff_workflow.png
data/bamExample.rda
data/barcodeExample.rda
data/cbtop10000.rda
data/sceExample.rda
data/validCb.rda
inst/NEWS
inst/extdata/GRCm38_MT.fa
inst/extdata/GRCm38_MT.gtf
inst/extdata/SRR5167880_E18_20160930_Neurons_Sample_01_5000.bam
inst/extdata/SRR5167880_E18_20160930_Neurons_Sample_01_filtered_barcode.tsv
inst/extdata/vandenBrink_1h1_L001_R1_001.fastq.gz
inst/extdata/vandenBrink_1h1_L001_R2_001.fastq.gz
man/alignRsubread.Rd
man/bamExample.Rd
man/barcodeExample.Rd
man/cbtop10000.Rd
man/countUMI.Rd
man/demultiplex.Rd
man/gview.Rd
man/qcplots.Rd
man/rview.Rd
man/sceExample.Rd
man/scruff.Rd
man/tenxBamqc.Rd
man/validCb.Rd
tests/testthat.R
tests/testthat/testscruff.R
vignettes/scruff.Rmd
