Files in FrietzeLabUVM/ssvQC
QC for enrichment based NGS
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/ClusteredSignal.R
R/QcConfig.R
R/QcConfigFeatures.R
R/QcConfigSignal.R
R/QcPlot.R
R/functions_bfcif.R
R/functions_diff.R
R/functions_make.R
R/functions_misc.R
R/functions_plot.R
R/functions_run_by_match.R
R/functions_scc.R
R/functions_write.R
R/onAttach.R
R/ssvQC.R
R/ssvQC_FRIP.R
R/ssvQC_SCC.R
R/ssvQC_capValue.R
R/ssvQC_correlation.R
R/ssvQC_features.R
R/ssvQC_fragLens.R
R/ssvQC_mappedReads.R
R/ssvQC_select.R
R/ssvQC_signal.R
R/vars.R
R/write.R
README.md
dev_alignement_locations.R
inst/extdata/CTCF_in_10a_overlaps.bed
inst/extdata/MCF10AT1_CTCF_FE_random100.bw
inst/extdata/MCF10AT1_CTCF_R1.100peaks.bam
inst/extdata/MCF10AT1_CTCF_R1.100peaks.bam.bai
inst/extdata/MCF10AT1_CTCF_random100.narrowPeak
inst/extdata/MCF10AT1_input_R1.100peaks.bam
inst/extdata/MCF10AT1_input_R1.100peaks.bam.bai
inst/extdata/MCF10A_CTCF_FE_random100.bw
inst/extdata/MCF10A_CTCF_R1.100peaks.bam
inst/extdata/MCF10A_CTCF_R1.100peaks.bam.bai
inst/extdata/MCF10A_CTCF_random100.narrowPeak
inst/extdata/MCF10A_input_R1.100peaks.bam
inst/extdata/MCF10A_input_R1.100peaks.bam.bai
inst/extdata/MCF10CA1_CTCF_FE_random100.bw
inst/extdata/MCF10CA1_CTCF_R1.100peaks.bam
inst/extdata/MCF10CA1_CTCF_R1.100peaks.bam.bai
inst/extdata/MCF10CA1_CTCF_random100.narrowPeak
inst/extdata/MCF10CA1_input_R1.100peaks.bam
inst/extdata/MCF10CA1_input_R1.100peaks.bam.bai
inst/extdata/gencode.v35.annotation.IKZF1.gtf
inst/extdata/gencode.v35.annotation.at_peaks.gtf
inst/extdata/ssvQC_bam_config.csv
inst/extdata/ssvQC_bigwig_config.csv
inst/extdata/ssvQC_peak_config.csv
inst/extdata/test_fastq.4_reads.fq
inst/extdata/test_fastq.4_reads.fq.cnt
inst/extdata/test_fastq.4_reads.fq.gz
inst/extdata/test_fastq.4_reads.fq.gz.cnt
inst/extdata/test_fastq.5_reads.fastq
inst/extdata/test_fastq.5_reads.fastq.cnt
inst/extdata/test_fastq.5_reads.fastq.gz
inst/extdata/test_fastq.5_reads.fastq.gz.cnt
inst/extdata/test_peaks.bam
inst/extdata/test_peaks.bam.bai
inst/extdata/test_peaks.bed
man/ClusteredSignal-class.Rd
man/ClusteredSignal.Rd
man/ClusteredSignal.fromConfig.Rd
man/ClusteredSignal.null.Rd
man/QcConfig.Rd
man/QcConfigFeatures.GRanges.Rd
man/QcConfigFeatures.Rd
man/QcConfigSignal.Rd
man/QcPlot-class.Rd
man/QcScaleColor-methods.Rd
man/bfcif.Rd
man/digest_args.Rd
man/dot-parse_config_header.Rd
man/dot-prepFeatures.Rd
man/dot-save_config.Rd
man/dot-show_QcConfig.Rd
man/dot-show_ssvQC.Rd
man/get_args.Rd
man/get_feature_file_load_function.Rd
man/get_mapped_reads.Rd
man/guess_feature_file_format.Rd
man/guess_read_mode.Rd
man/harmonize_seqlengths.Rd
man/make_anno_dt.Rd
man/make_anno_grs.Rd
man/make_assign_dt.Rd
man/make_centered_query_gr.Rd
man/make_dt.Rd
man/make_feature_as_signal_dt.Rd
man/make_feature_overlap_signal_profiles.Rd
man/make_fq_dt.Rd
man/make_frip_dt.Rd
man/make_peak_dt.Rd
man/make_scc_dt.Rd
man/make_scc_dt.single.Rd
man/parse_fetch_options.Rd
man/plot_anno_overlap.Rd
man/plot_feature_comparison.Rd
man/plot_feature_overlap_signal_profiles.Rd
man/plot_fq_dt.Rd
man/plot_frip_dt.Rd
man/plot_scc_dt.Rd
man/plot_signals.Rd
man/sampleCap.Rd
man/ssvQC.Rd
man/ssvQC.removeFeatures.Rd
man/ssvQC.save_config.Rd
man/ssvQC.selectClusters.Rd
man/ssv_mclapply.Rd
man/sync_height.Rd
man/sync_width.Rd
man/write_bed_frip.Rd
man/write_bed_overlaps.Rd
man/write_ssvQC.Rd
ref_code/AR_ATAC_qc.Rmd
ref_code/CG_k4me3_qc.Rmd
ref_code/CG_k4me3_with_AF_qc.Rmd
ref_code/MM_CTCF_qc.Rmd
ref_code/PR_mm10_bcells_cutnrun_selected_Ikaros_with_ATAC.Rmd
ref_code/ssvQC_paper_Ikaros.Rmd
ref_code/ssvQC_paper_Ikaros.fig2.Rmd
ref_code/ssvQC_paper_Ikaros.fig3.Rmd
ref_code/ssvQC_paper_Ikaros.pilot.Rmd
ssvQC.Rproj
tests/testthat.R
tests/testthat/test_bugfix.R
tests/testthat/test_center_and_high_on.R
tests/testthat/test_constructors.R
tests/testthat/test_digest_args.R
tests/testthat/test_remove_select.R
tests/testthat/test_run_ssvQC.R
tests/testthat/test_unique_names.R
vignettes/qc_feature_config.csv
vignettes/qc_signal_config.csv
vignettes/ssvQC_demo.Rmd
