Files in vanheeringen-lab/learnr.proto
A set of LearnR Tutorials.
.Rbuildignore
.Renviron
.Rprofile
.gitignore
DESCRIPTION
NAMESPACE
R/functions.R
R/prep_week2.R
README.md
docs/christa/1_preparing_track_hubs.docx
docs/christa/2_20200106_selectchr19_in_bigwigfiles.docx
docs/christa/3_prepdata.html
docs/christa/4_fg1_file_lcoation
docs/christa/5_links_youtube_genomebrowser_tutorials
docs/siebren/1_overview_tools.docx
docs/siebren/1_overview_tools.xlsx
docs/siebren/2_RstudioServer_vs_ShinyServer.docx
docs/siebren/3_tutorial_framework.docx
docs/siebren/4_library_permissions.docx
docs/siebren/5_progress_tracking.docx
docs/siebren/6_code_checking.docx
docs/siebren/7_library_environment.docx
docs/siebren/8_data.docx
docs/siebren/9_minimal_startup_script.docx
inst/extdata/README.txt
inst/extdata/prepdata_20210216.Rmd
inst/extdata/tips_howtos_etc_writtenby_christa_toenhake.Rmd
inst/extdata/week2.Rdata
inst/extdata/week2/encode/gencodev32.chr19.bed
inst/extdata/week2/prepared_rds/blueprint_c000s5_gene_quantification_chr19.rds
inst/extdata/week2/prepared_rds/blueprint_monocyte_chr19_granges.RData
inst/extdata/week2/prepared_rds/gene_entrezids_genesymbols_df.rds
inst/extdata/week3.Rdata
inst/extdata/week3/bw_chr19_tss_sample/C000S5H2.ERX547980.H3K27ac.bwa.GRCh38.20150528.chr19_chr19tss_60Genes_10kb.bw
inst/extdata/week3/bw_chr19_tss_sample/C000S5H2.ERX547981.H3K4me1.bwa.GRCh38.20150528.chr19_chr19tss_60Genes_10kb.bw
inst/extdata/week3/bw_chr19_tss_sample/C000S5H2.ERX547983.H3K27me3.bwa.GRCh38.20150528.chr19_chr19tss_60Genes_10kb.bw
inst/extdata/week3/bw_chr19_tss_sample/C000S5H2.ERX547984.H3K4me3.bwa.GRCh38.20150528.chr19_chr19tss_60Genes_10kb.bw
inst/tutorials/fg1/css/custom.css
inst/tutorials/fg1/css/print2pdf.css
inst/tutorials/fg1/fg1.Rmd
inst/tutorials/fg1/images/index_fig1_plosbiol_2011_ENCODE_userguid_fig1_original.png
inst/tutorials/fg1/images/index_fig1_plosbiol_2011_ENCODE_userguid_fig1a.png
inst/tutorials/fg1/images/index_fig2_BP_Haematopoiesis_original.pdf
inst/tutorials/fg1/images/index_fig2_BP_Haematopoiesis_original.png
inst/tutorials/fg1/images/wk1_1_flowcell.png
inst/tutorials/fg1/images/wk1_1_illuminalibrary.png
inst/tutorials/fg1/images/wk1_1_illuminasequencing.jpg
inst/tutorials/fg1/images/wk1_1_illuminasequencing.png
inst/tutorials/fg1/images/wk1_1_phred_ascii.png
inst/tutorials/fg1/images/wk1_1_sequencing_library_structure_barbrahamcourse.png
inst/tutorials/fg1/images/wk1_2_fastq_layout.png
inst/tutorials/fg1/images/wk1_2_phred_quality_scores_TorstenSeemannpresentation.png
inst/tutorials/fg1/images/wk1_2_wiki_genestructure_updownstream.png
inst/tutorials/fg1/images/wk1_3_BAM_fields_broadinstitute.png
inst/tutorials/fg1/images/wk1_3_Furay_2012_naturereviews_fig2_chipseqanalysis.png
inst/tutorials/fg1/images/wk1_3_bam_header_example_sandrews_tutorial201911.png
inst/tutorials/fg1/images/wk1_3_bam_record_example_sandrews_tutorial201911.png
inst/tutorials/fg1/images/wk1_3_bedgraph_format_bedgraph.png
inst/tutorials/fg1/images/wk1_3_chipseq_workflow_nakato2020methods.jpg
inst/tutorials/fg1/images/wk1_3_chipseq_workflow_utsoutwesternedu_mcdermottlab.png
inst/tutorials/fg1/images/wk1_3_encode_chipseq_readmapping.png
inst/tutorials/fg1/images/wk1_3_ex1_fastqc_per_base_quality_example1.png
inst/tutorials/fg1/images/wk1_3_ex1_fastqc_per_base_quality_example2.png
inst/tutorials/fg1/images/wk1_3_fairdata_fosteropenscience.png
inst/tutorials/fg1/images/wk1_3_fastqc_per_base_quality_bad.png
inst/tutorials/fg1/images/wk1_3_fastqc_per_base_quality_good.png
inst/tutorials/fg1/images/wk1_3_fastqc_per_base_quality_vb1.png
inst/tutorials/fg1/images/wk1_3_fastqc_per_base_quality_vb2.png
inst/tutorials/fg1/images/wk1_3_file_format_bed.png
inst/tutorials/fg1/images/wk1_3_file_format_gff.png
inst/tutorials/fg1/images/wk1_3_intro_whatbioinformaticiancsdo.png
inst/tutorials/fg1/images/wk1_3_narrowpeakfile_layout.png
inst/tutorials/fg1/images/wk1_3_read_depth_Pavlopoulos2018.png
inst/tutorials/fg1/images/wk1_3_sample_clustering_siebrenspptx.svg
inst/tutorials/fg1/images/wk1_3_seq2science_siebrenspptx.png
inst/tutorials/fg1/images/wk1_4_gb_configure.png
inst/tutorials/fg1/images/wk1_4_gb_configureImage.png
inst/tutorials/fg1/images/wk1_4_gb_configure_track_display.png
inst/tutorials/fg1/images/wk1_4_gb_drag_and_select.png
inst/tutorials/fg1/images/wk1_4_upstream_downstream_munca.jpg
inst/tutorials/fg1/images/wk1_4b_ucsc_gb_actb_geneinformation.png
inst/tutorials/fg1/images/wk1_4b_ucsc_gb_actb_genetracksonly.png
inst/tutorials/fg1/images/wk1_4b_ucsc_gb_actb_locationinchromosome.png
inst/tutorials/fg1/images/wk1_4b_ucsc_gb_actb_question_TSSquestion.png
inst/tutorials/fg1/images/wk1_4b_ucsc_gb_actb_question_startpage.png
inst/tutorials/fg1/images/wk1_4b_ucsc_gb_unselectsplicevariants.png
inst/tutorials/fg1/images/wk1_4b_ucsc_genome_browser_topmenubar.png
inst/tutorials/fg1/images/wk1_4c_ucsc_gb_encode_fig1_gototrackhub.png
inst/tutorials/fg1/images/wk1_4c_ucsc_gb_encode_fig2_trackhub.png
inst/tutorials/fg1/images/wk1_4d_sessions_no_sessionsyet.png
inst/tutorials/fg1/images/wk1_4d_sessions_saved.png
inst/tutorials/fg1/images/wk1_4d_sessions_saving.png
inst/tutorials/fg2/css/custom.css
inst/tutorials/fg2/css/print2pdf.css
inst/tutorials/fg2/fg2.Rmd
inst/tutorials/fg2/images/wk1_3_file_format_bed.png
inst/tutorials/fg2/images/wk1_3_file_format_gff.png
inst/tutorials/fg2/images/wk2_2_GRanges_fields_my_gr.png
inst/tutorials/fg2/images/wk2_3_ggplottemplate.png
inst/tutorials/fg2/images/wk2_4_complexheatmap_modes.png
inst/tutorials/fg2/images/wk2_5_upsetplots_q13.png
inst/tutorials/fg2/images/wk2_5_upsetplots_q14.png
inst/tutorials/fg2/images/wk2_6_set_example.png
inst/tutorials/fg2/images/wk2_6_set_example_upset.png
inst/tutorials/fg2/images/wk2_6_set_example_venn.png
inst/tutorials/fg2/images/wk2_6_upset_with_fpkm.png
inst/tutorials/fg2/images/wk2_6_venn_6set_banana.png
inst/tutorials/fg3/css/custom.css
inst/tutorials/fg3/css/print2pdf.css
inst/tutorials/fg3/fg3.Rmd
inst/tutorials/fg3/images/boxplot_average_h3k4me3_tss_5kbwindow_genegroup_withcolors.png
inst/tutorials/fg3/images/emissions_12_Blueprint_release_20160816_forex16.png
inst/tutorials/fg3/images/genomation_scorematrix.png
inst/tutorials/fg3/images/q10b_heatmap_h3k4me3signal_ordered.png
inst/tutorials/fg3/images/q14b_heatmap_h3k4me3_h3k27me3_signal_fpkmordered.png
inst/tutorials/fg3/images/q15c_heatmap_h3k4me3_h3k27ac_h2k4me1_h3k27me3_signal_fpkmordered.png
inst/tutorials/fg3/images/q3b_averageprofile_h3k4me3_tss.png
inst/tutorials/fg3/images/q4_averageprofile_h3k27ac_tss.png
inst/tutorials/fg3/images/q6_averageprofile_overlay_tss.png
inst/tutorials/fg3/images/q7b_boxplot_average_h3k4me3_tss_5kbwindow.png
inst/tutorials/fg3/images/q7e_scatterplot_average_h3k4me3_tss_5kbwindow_vs_fpkm_incl_default_smoothline.png
inst/tutorials/fg3/images/q7e_scatterplot_average_h3k4me3_tss_5kbwindow_vs_fpkm_incl_lm_fitline.png
inst/tutorials/fg3/images/q9b_heatmap_h3k4me3signal.png
inst/tutorials/template/css/custom.css
inst/tutorials/template/css/print2pdf.css
inst/tutorials/template/template.Rmd
inst/tutorials/test/css/custom.css
inst/tutorials/test/css/print2pdf.css
inst/tutorials/test/images/cats.jpg
inst/tutorials/test/test.Rmd
renv.lock
renv/.gitignore
renv/activate.R
renv/settings.dcf
