Files in scPipe
pipeline for single cell RNA-seq data analysis

DESCRIPTION
README.md
.BBSoptions
NAMESPACE
inst/workflow.png
inst/scPipe.png
inst/NEWS.Rd
inst/doc/scPipe_tutorial.html
inst/doc/scPipe_tutorial.R inst/doc/scPipe_tutorial.Rmd
inst/extdata/ERCC92_anno.gff3
inst/extdata/ensembl_y_tiny.gtf.gz
inst/extdata/gen_tiny_anno.gff3.gz
inst/extdata/simu_R1.fastq.gz
inst/extdata/report_template_slim.Rmd
inst/extdata/ens_tiny_anno.gff3.gz
inst/extdata/simu_R2.fastq.gz
inst/extdata/report_template.Rmd
inst/extdata/ref_tiny_anno.gff3.gz
inst/extdata/barcode_anno.csv
inst/extdata/ensembl_hg38_chrY.gtf.gz
inst/extdata/ens_tiny_anno.gtf.gz
inst/extdata/ERCC92.fa
inst/extdata/gen_tiny_anno.gtf.gz
vignettes/scPipe_tutorial.Rmd R/qc.R R/anno_import.R R/biomart_methods.R R/help.R R/utils.R R/get_read_str.R R/RcppExports.R R/SCE_methods.R R/catch-routine-registration.R R/sc_sample_data.R R/wrapper_scPipeCPP.R R/AllGenerics.R R/sc_workflow.R R/sc_sample_qc.R
src/cellbarcode.cpp
src/parsebam.cpp
src/trimbarcode.cpp
src/parsebam.h
src/parsecount.h
src/Timer.h
src/parsecount.cpp
src/transcriptmapping.cpp
src/Makevars.win
src/global_config.h
src/detect_barcode.h
src/detect_barcode.cpp
src/rcpp_scPipe_func.cpp
src/utils.cpp
src/RcppExports.cpp
src/transcriptmapping.h
src/Gene.h
src/cellbarcode.h
src/Interval.h
src/utils.h
src/test-runner.cpp
src/config_hts.h
src/trimbarcode.h
src/Makevars
src/Interval.cpp
src/Gene.cpp
src/test-cpp.cpp
man/get_read_str.Rd man/sc_detect_bc.Rd man/sc_exon_mapping.Rd man/calculate_QC_metrics.Rd man/convert_geneid.Rd man/anno_import.Rd man/get_ercc_anno.Rd man/plot_mapping.Rd man/UMI_duplication.Rd man/gene_id_type.Rd man/sc_gene_counting.Rd man/anno_to_saf.Rd man/cell_barcode_matching.Rd man/sc_sample_qc.Rd man/create_report.Rd man/detect_outlier.Rd man/sc_demultiplex.Rd man/QC_metrics.Rd man/plot_UMI_dup.Rd man/plot_QC_pairs.Rd man/scPipe.Rd man/remove_outliers.Rd man/UMI_dup_info.Rd man/create_sce_by_dir.Rd man/get_genes_by_GO.Rd man/sc_trim_barcode.Rd man/plot_demultiplex.Rd man/sc_sample_data.Rd man/sc_count_aligned_bam.Rd man/sc_demultiplex_and_count.Rd man/organism.Rd man/demultiplex_info.Rd man/dot-qq_outliers_robust.Rd man/create_processed_report.Rd
build/vignette.rds
tests/testthat.R tests/testthat/test-cpp.R tests/testthat/test_sce.R tests/testthat/test-import_anno.R tests/testthat/test-get_read_str.R
data/sc_sample_qc.RData
data/sc_sample_data.RData
scPipe documentation built on Oct. 31, 2019, 6:01 a.m.