Files in jrboyd/ssvRecipes
Recipes using seqsetvis
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/function_fix_xlsx_dates.R
R/function_truncate_peak_file.R
R/functions_GR_ovlerlaps.R
R/functions_RNAseq_counts.R
R/functions_RNAseq_salmon.R
R/functions_alignment_mismatch.R
R/functions_bfcif.R
R/functions_bigwig_correlation.R
R/functions_bw_cluster_summary.R
R/functions_clusterProfiler.R
R/functions_corrDiff.R
R/functions_fetchBamPE.R
R/functions_file_helpers.R
R/functions_hclust.R
R/functions_heatmap_with_sideplots.R
R/functions_load_STAR_RNA_counts.R
R/functions_multimapping.R
R/functions_my_files.R
R/functions_plot_ideogram.R
R/functions_sample.R
R/functions_scRNA_fetch.R
R/functions_scRNAseq.R
R/functions_scatter_with_side_density.R
R/functions_scatterplot_with_side_density.R
R/functions_stranded_bamFetch.R
R/functions_syncDims.R
R/functions_timestamps.R
R/functions_tracks.R
data/GTF_TO_FASTA_PATH.rda
data/HG38_SEQ_PATH.rda
data/HG38_SEQ_URL.rda
data/HG38_STAR_INDEX.rda
data/HG38_v28_GTF_URL.rda
data/SALMON_PATH.rda
data/STAR_PATH.rda
data/dt_rna.rda
data/heatmap_demo_matrix.rda
dev_bam_alignment.R
dev_ontology.R
dev_viral_snapshots.R
inst/extdata/pcaOut.PC1.chr2x.txt
inst/extdata/testPE.bam
inst/extdata/testPE.bam.bai
inst/extdata/test_1.ReadsPerGene.out.tab
inst/extdata/test_2.ReadsPerGene.out.tab
inst/extdata/test_3.ReadsPerGene.out.tab
inst/extdata/test_bad.ReadsPerGene.out.tab
inst/extdata/test_second.ReadsPerGene.out.tab
man/alignFasta.Rd
man/annotate_gr.Rd
man/annotate_gr_clusters.Rd
man/bfcif.Rd
man/cache_FUN.Rd
man/cache_gz.Rd
man/corr_fragLens.Rd
man/corr_fragLens.single.Rd
man/counts_from_bams.Rd
man/dot-get_files.Rd
man/fetch_bw_summary.Rd
man/fix_xlsx_dates.Rd
man/gene_name_hs2mm.Rd
man/get_gg_xrange.Rd
man/get_gg_yrange.Rd
man/get_hclust_gls.Rd
man/get_meta_dt.Rd
man/get_my_files.Rd
man/get_rna_dt.Rd
man/ggheatmap.dendro.Rd
man/gr_distance_overlap.Rd
man/guess_lib_from_file.Rd
man/h.cluster_data.Rd
man/h.cluster_members.Rd
man/h.final_plot.Rd
man/h.plot_parts_grouped.Rd
man/h.plot_parts_individual.Rd
man/is_gz.Rd
man/is_url.Rd
man/kill_jids.Rd
man/load_matrix_from_ReadsPerGene.out.tab.Rd
man/make_cell_dt_from_list.Rd
man/make_msigdb_TERM2GENE.Rd
man/myFetchStrandedBam.Rd
man/myPlotDiffClusters.Rd
man/myStrandDiff.Rd
man/my_clusterProfiler_GO.Rd
man/my_clusterProfiler_KEGG.Rd
man/my_clusterProfiler_MSigDB.Rd
man/my_clusterProfiler_table.Rd
man/parse_xls.Rd
man/parse_xls_reads.Rd
man/plot-methods.Rd
man/plotHomerKnowResults.Rd
man/plot_bam_mismatch_dt.Rd
man/plot_hclust_heatmap.Rd
man/plot_hclust_heatmap.assemble.Rd
man/plot_scatter_side_density.Rd
man/plot_scatter_side_density.assemble.Rd
man/plot_scatter_side_density.xy.Rd
man/read.table.fix_xlsx_dates.Rd
man/reorderHeatmapClusters.Rd
man/rnaseq_asses_strandedness.Rd
man/running_jids.Rd
man/salmon_index_transcriptome.Rd
man/salmon_tx_quant.Rd
man/sampleCap.Rd
man/show-methods.Rd
man/ssvFetchBam.scRNA.Rd
man/ssvFetchBamPE.RNA.Rd
man/ssvH2-class.Rd
man/ssvHeatmap2.Rd
man/ssvR_plot_bam_mismatch.Rd
man/ssvR_plot_ideogogram.Rd
man/ssvR_plot_ideogogram_data.Rd
man/star_align_fastq_PE.Rd
man/star_align_fastq_SE.Rd
man/star_align_fastq_core.Rd
man/symbol2uniprot.Rd
man/sync_height.Rd
man/sync_width.Rd
man/timestamp.mdy.Rd
man/track_assembly.Rd
man/track_chip.Rd
man/track_ref.Rd
man/track_rna.Rd
man/truncate_peak_file.Rd
man/wait_jids.Rd
man/watch_jids.Rd
man/writeBigBed.Rd
man/writeFastaFromGR.Rd
man/writeFastaFromSeq.Rd
man/write_geneList_matrix.Rd
ssvRecipes.Rproj
vignettes/demo_heatmap_with_sideplots.Rmd
vignettes/rnaseq_analysis.Rmd
