Files in LuyiTian/scPipe
Pipeline for single cell multi-omic data pre-processing
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/AllGenerics.R
R/RcppExports.R
R/SCE_methods.R
R/anno_import.R
R/basilisk.R
R/biomart_methods.R
R/catch-routine-registration.R
R/check_barcode_start.R
R/get_read_str.R
R/help.R
R/qc.R
R/sc_aligning.R
R/sc_atac_bam_tagging.R
R/sc_atac_cell_calling.R
R/sc_atac_create_cell_qc_metrics.R
R/sc_atac_create_fragments.R
R/sc_atac_create_report.R
R/sc_atac_create_sce.R
R/sc_atac_feature_counting.R
R/sc_atac_peak_calling.R
R/sc_atac_pipeline.R
R/sc_atac_remove_duplicates.R
R/sc_atac_subfunctions.R
R/sc_atac_tfidf.R
R/sc_atac_trim_barcode.R
R/sc_integrate.R
R/sc_sample_data.R
R/sc_sample_qc.R
R/sc_workflow.R
R/utils.R
R/wrapper_scPipeCPP.R
R/zzz.R
README.md
data/sc_sample_data.RData
data/sc_sample_qc.RData
inst/.Rapp.history
inst/CITATION
inst/NEWS.Rd
inst/extdata/ERCC92.fa
inst/extdata/ERCC92_anno.gff3
inst/extdata/NA_peaks.narrowPeak
inst/extdata/annotations/chrom_hg19.sizes.gz
inst/extdata/annotations/chrom_hg38.sizes.gz
inst/extdata/annotations/chrom_mm10.sizes.gz
inst/extdata/annotations/hg19_blacklist.bed.gz
inst/extdata/annotations/hg19_enhancer.bed.gz
inst/extdata/annotations/hg19_promoter.bed.gz
inst/extdata/annotations/hg19_tss.bed.gz
inst/extdata/annotations/hg38_blacklist.bed.gz
inst/extdata/annotations/hg38_enhancer.bed.gz
inst/extdata/annotations/hg38_promoter.bed.gz
inst/extdata/annotations/hg38_tss.bed.gz
inst/extdata/annotations/mm10_blacklist.bed.gz
inst/extdata/annotations/mm10_enhancer.bed.gz
inst/extdata/annotations/mm10_promoter.bed.gz
inst/extdata/annotations/mm10_tss.bed.gz
inst/extdata/barcode_anno.csv
inst/extdata/chr21_modified_barcode_1000.csv
inst/extdata/ens_tiny_anno.gff3.gz
inst/extdata/ens_tiny_anno.gtf.gz
inst/extdata/ensembl_hg38_chrY.gtf.gz
inst/extdata/ensembl_y_tiny.gtf.gz
inst/extdata/gen_tiny_anno.gff3.gz
inst/extdata/gen_tiny_anno.gtf.gz
inst/extdata/ref_tiny_anno.gff3.gz
inst/extdata/report_template.Rmd
inst/extdata/report_template_slim.Rmd
inst/extdata/rmd_report_skeleton.Rmd
inst/extdata/sc-atac-sample-feature-matrix.RDS
inst/extdata/sc-atac-sample-sparse-matrix.RDS
inst/extdata/simu_R1.fastq.gz
inst/extdata/simu_R2.fastq.gz
inst/extdata/small_chr21.fa
inst/extdata/small_chr21.fa.fai
inst/extdata/small_chr21_R1.fastq.gz
inst/extdata/small_chr21_R2.fastq.gz
inst/extdata/small_chr21_R3.fastq.gz
inst/extdata/smallbarcode1col.csv
inst/report_example.png
inst/scATAC-seq_workflow.png
inst/scPipe.png
inst/workflow.png
inst/workflow_combined.png
man/QC_metrics.Rd
man/TF.IDF.custom.Rd
man/UMI_dup_info.Rd
man/UMI_duplication.Rd
man/anno_import.Rd
man/anno_to_saf.Rd
man/calculate_QC_metrics.Rd
man/cell_barcode_matching.Rd
man/check_barcode_start_position.Rd
man/convert_geneid.Rd
man/create_processed_report.Rd
man/create_report.Rd
man/create_sce_by_dir.Rd
man/demultiplex_info.Rd
man/detect_outlier.Rd
man/dot-qq_outliers_robust.Rd
man/feature_info.Rd
man/feature_type.Rd
man/gene_id_type.Rd
man/get_chromosomes.Rd
man/get_ercc_anno.Rd
man/get_genes_by_GO.Rd
man/get_read_str.Rd
man/organism.Rd
man/plot_QC_pairs.Rd
man/plot_UMI_dup.Rd
man/plot_demultiplex.Rd
man/plot_mapping.Rd
man/read_cells.Rd
man/remove_outliers.Rd
man/scPipe.Rd
man/sc_aligning.Rd
man/sc_atac_bam_tagging.Rd
man/sc_atac_cell_calling.Rd
man/sc_atac_create_cell_qc_metrics.Rd
man/sc_atac_create_fragments.Rd
man/sc_atac_create_report.Rd
man/sc_atac_create_sce.Rd
man/sc_atac_emptydrops_cell_calling.Rd
man/sc_atac_feature_counting.Rd
man/sc_atac_filter_cell_calling.Rd
man/sc_atac_peak_calling.Rd
man/sc_atac_pipeline.Rd
man/sc_atac_pipeline_quick_test.Rd
man/sc_atac_plot_cells_per_feature.Rd
man/sc_atac_plot_features_per_cell.Rd
man/sc_atac_plot_features_per_cell_ordered.Rd
man/sc_atac_plot_fragments_cells_per_feature.Rd
man/sc_atac_plot_fragments_features_per_cell.Rd
man/sc_atac_plot_fragments_per_cell.Rd
man/sc_atac_plot_fragments_per_feature.Rd
man/sc_atac_remove_duplicates.Rd
man/sc_atac_tfidf.Rd
man/sc_atac_trim_barcode.Rd
man/sc_correct_bam_bc.Rd
man/sc_count_aligned_bam.Rd
man/sc_demultiplex.Rd
man/sc_demultiplex_and_count.Rd
man/sc_detect_bc.Rd
man/sc_exon_mapping.Rd
man/sc_gene_counting.Rd
man/sc_get_umap_data.Rd
man/sc_integrate.Rd
man/sc_interactive_umap_plot.Rd
man/sc_mae_plot_umap.Rd
man/sc_sample_data.Rd
man/sc_sample_qc.Rd
man/sc_trim_barcode.Rd
minimal_atac_example.md
src/.gitignore
src/FragmentThread.cpp
src/FragmentThread.h
src/FragmentUtils.cpp
src/FragmentUtils.h
src/Fragments.h
src/Gene.cpp
src/Gene.h
src/Interval.cpp
src/Interval.h
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/ResizeArray.cpp
src/ResizeArray.h
src/ThreadOutputFile.cpp
src/ThreadOutputFile.h
src/Timer.h
src/Trie.cpp
src/Trie.h
src/__pycache__/sinto_fragments.cpython-36.pyc
src/__pycache__/utils.cpython-36.pyc
src/bam.c
src/bam.h
src/cellbarcode.cpp
src/cellbarcode.h
src/check_barcode_reads.cpp
src/config_hts.h
src/detect_barcode.cpp
src/detect_barcode.h
src/global_config.h
src/parsebam.cpp
src/parsebam.h
src/parsecount.cpp
src/parsecount.h
src/qc_per_bc_file_helper.cpp
src/rcpp_scPipe_func.cpp
src/sam_header.h
src/sc_atac_create_fragments.cpp
src/sc_atac_create_fragments.h
src/test-cpp.cpp
src/test-example.cpp
src/test-fragmentThread.cpp
src/test-resizearray.cpp
src/test-runner.cpp
src/test-trie_matching.cpp
src/transcriptmapping.cpp
src/transcriptmapping.h
src/trimbarcode.cpp
src/trimbarcode.h
src/tsscreatebins.cpp
src/utils.cpp
src/utils.h
tests/testthat.R
tests/testthat/test-anno_import.R
tests/testthat/test-check_barcode_reads.R
tests/testthat/test-cpp.R
tests/testthat/test-get_read_str.R
tests/testthat/test_sce.R
vignettes/scPipe_atac_tutorial.R
vignettes/scPipe_atac_tutorial.Rmd
vignettes/scPipe_atac_tutorial.html
vignettes/scPipe_tutorial.R
vignettes/scPipe_tutorial.Rmd
vignettes/scPipe_tutorial.html
