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