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

LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.