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
jiang-junyao/IReNA documentation built on Nov. 15, 2024, 1:51 a.m.