Files in jiang-junyao/IReNA
IReNA
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/ATAC-seq.R
R/Footprints_FOS.R
R/ID_change.R
R/annotation.R
R/data.r
R/filter_fimo.R
R/main_pipeline.R
R/matchmotif.R
R/merge_footprints.R
R/network_visualization.R
R/preprocess.R
R/reconstruct_network.R
R/scATAC.R
R/scRNA1.R
R/smooth.R
R/validation.R
R/wig_track.R
README.Rmd
README.md
data/ChscRNA_genes.rda
data/HsscRNA_genes.rda
data/MmscRNA_genes.rda
data/Tranfac201803_Ch_MotifTFsF.rda
data/Tranfac201803_Hs_MotifTFsF.rda
data/Tranfac201803_Mm_MotifTFsF.rda
data/Tranfac201803_Zf_MotifTFsF.rda
data/Transfac_PWMatrixList.rda
data/ZfscRNA_genes.rda
data/hg38_gene_tss.rda
data/mm10_gene_tss.rda
docs/ATAC-seq-preprocessing.html
docs/Readme figure/CM_Cytoscape_intramodular.png
docs/Readme figure/CM_Cytoscape_network.png
docs/Readme figure/CM_Kmeans_plot.png
docs/Readme figure/CM_intermodular_network.png
docs/Readme figure/CM_tf_network.png
docs/Readme figure/Cytoscape_intramodular.png
docs/Readme figure/Cytoscape_network.png
docs/Readme figure/Kmeans_plot.png
docs/Readme figure/Workflow.png
docs/Readme figure/Workflow1.png
docs/Readme figure/bulk_Cytoscape_intramodular.png
docs/Readme figure/bulk_Cytoscape_network.png
docs/Readme figure/bulk_atac_intramodular_network.png
docs/Readme figure/bulk_atac_tf_network.png
docs/Readme figure/intramodular_network.png
docs/Readme figure/significance.png
docs/Readme figure/tf_network.png
docs/Readme figure/workflow_new.jpg
docs/_config.yml
docs/bulk-ATAC+scRNA.html
docs/only-scRNA.html
docs/qucik-start.html
docs/qucik-start2.html
docs/scATAC+scRNA.html
docs/scATAC-seq-preprocessing.html
docs/scRNA-seq-preprocessing.html
docs/tutorial.html
inst/extdata/CM_exp.rda
inst/extdata/Candid.rda
inst/extdata/combined.rda
inst/extdata/fdr005.rda
inst/extdata/gene_tss.rda
inst/extdata/list1.rda
inst/extdata/qucik_start_test.rda
inst/extdata/test_clustering.rda
inst/extdata/test_peak.rda
inst/extdata/test_seurat.rda
inst/extdata/wig_list.rda
man/ChscRNA_genes.Rd
man/Converse_GeneIDSymbol.Rd
man/Footprints_FOS.Rd
man/Get_p2g_fun.Rd
man/HsscRNA_genes.Rd
man/MmscRNA_genes.Rd
man/Tranfac201803_Ch_MotifTFsF.Rd
man/Tranfac201803_Hs_MotifTFsF.Rd
man/Tranfac201803_Mm_MotifTFsF.Rd
man/Tranfac201803_Zf_MotifTFsF.Rd
man/ZfscRNA_genes.Rd
man/add_ENSID.Rd
man/add_pseudotime.Rd
man/add_regulation_type.Rd
man/cal_footprint_cuts.Rd
man/clustering_Kmeans.Rd
man/combine_footprints.Rd
man/diff_peaks.Rd
man/enrich_module.Rd
man/extract_expressed_TFs.Rd
man/filter_ATAC.Rd
man/filter_expression_profile.Rd
man/filter_original_regulation.Rd
man/filter_regulation_Rcis.Rd
man/filter_regulation_fimo.Rd
man/find_motifs.Rd
man/find_motifs_targetgenes.Rd
man/generate_fimo_regulation.Rd
man/generate_peak_gtf.Rd
man/generate_scATAC_Candid.Rd
man/get_SmoothByBin_PseudotimeExp.Rd
man/get_bed.Rd
man/get_cor.Rd
man/get_merged_fasta.Rd
man/get_pseudotime.Rd
man/get_related_genes.Rd
man/get_related_peaks.Rd
man/get_tss_region.Rd
man/identify_region_tfs.Rd
man/initiate_cy.Rd
man/irena_step1.Rd
man/irena_step2.Rd
man/load_counts.Rd
man/merge_sort_count.Rd
man/motifs_select.Rd
man/network_analysis.Rd
man/output_grn.Rd
man/overlap_footprints_peaks.Rd
man/plot_intramodular_network.Rd
man/plot_kmeans_pheatmap.Rd
man/plot_tf_network.Rd
man/sort_TFs_degree.Rd
tests/testthat.R
tests/testthat/Rplots.pdf
tests/testthat/test-test_pipline.R
tests/testthat/test-test_scRNA.R
