├── .TOUCH ├── .github └── pull-request-template.md ├── .gitignore ├── ExploratoryAnalysis.Rmd ├── ExploratoryAnalysis.html ├── Intro_to_Cluster.md ├── LICENSE ├── Makefile ├── RNA-seq-Analysis.md ├── R_Intro_Lesson.Rmd ├── R_Intro_Lesson.html ├── R_Intro_Lesson.md ├── StatsNstuff.pdf ├── _static ├── ChIPseq.2400x2400.jpeg ├── DESeq2_workflow.png ├── ERR458493.qc_fastqc.html ├── ERR458493_fastqc.html ├── ERR458500.qc_fastqc.html ├── ERR458500_fastqc.html ├── GCA_000146045.2_R64_tx2gene.tsv ├── Lee-5-things.pdf ├── Lemd1.2400x2400.jpeg ├── RStudio.png ├── RStudio_create_R_script.png ├── RStudio_first.png ├── RStudio_type_script.png ├── Sourmash_flow_diagrams_QC.png ├── Sourmash_flow_diagrams_QC.thumb.png ├── Sourmash_flow_diagrams_compare.png ├── Sourmash_flow_diagrams_compare.thumb.png ├── Sourmash_flow_diagrams_compute.png ├── Sourmash_flow_diagrams_compute.thumb.png ├── Sourmash_flow_diagrams_gather.png ├── Sourmash_flow_diagrams_gather.thumb.png ├── Sourmash_flow_diagrams_search.png ├── Sourmash_flow_diagrams_search.thumb.png ├── UCSC1.2400x2400.jpeg ├── UCSC2.2400x2400.jpeg ├── UCSC3.2400x2400.jpeg ├── amplicon_overview.png ├── bam_file.png ├── bash-script-01.png ├── bash-script-01a.png ├── bash-script-02.png ├── bash-script-02a.png ├── bash-script-02b.png ├── bash-script-03.png ├── bash-script-04.png ├── binder │ ├── install.R │ └── runtime.txt ├── blast-ex.png ├── blastp-B-cep.png ├── blastviz.png ├── cloud_compute.png ├── conda1.png ├── conda2.png ├── conda3.png ├── conda4.png ├── conda5.png ├── dag_multiple.png ├── dag_one.png ├── de-novo-post-trim-R1-fastqc.html ├── de-novo-post-trim-R2-fastqc.html ├── de-novo-pre-trim-R1-fastqc.html ├── de-novo-pre-trim-R2-fastqc.html ├── de-novo-quast.html ├── de_theory.png ├── deseq_heatmap.png ├── deseq_ma.png ├── deseq_mds.png ├── deseq_pca.png ├── deseq_rdn18.png ├── dist_syn.png ├── ecoli_cmp.matrix.png ├── ecoli_cmp.matrix.thumb.png ├── ensemble1.png ├── ensemble2.png ├── ensemble3.png ├── ensemble4.png ├── envs.png ├── explicit_coding.png ├── fastqc_R1_before.png ├── fastqc_R2_before.png ├── fastqc_after.png ├── first_lines.png ├── fresh_anvi.png ├── gen_from_metagen_slide.png ├── gfp.2400x2400.jpeg ├── ggplot-1.png ├── ggplot-10.png ├── ggplot-11.png ├── ggplot-12.png ├── ggplot-13.png ├── ggplot-14.png ├── ggplot-15.png ├── ggplot-16.png ├── ggplot-17.png ├── ggplot-18.png ├── ggplot-2.png ├── ggplot-3.png ├── ggplot-4.png ├── ggplot-5.png ├── ggplot-6.png ├── ggplot-7.png ├── ggplot-8.png ├── ggplot-8b.png ├── ggplot-9.png ├── git │ ├── merge.svg │ ├── phd101212s.gif │ ├── play-changes.svg │ └── versions.svg ├── git_PR.png ├── git_branch.png ├── git_create_repo.png ├── git_issues.png ├── git_new_repo.png ├── git_octocat.png ├── git_overview.png ├── git_remote.png ├── git_working.png ├── github_commit.png ├── github_repo.png ├── implicit_coding.png ├── jet_actions.png ├── jet_dashboard.png ├── jet_links.png ├── join.png ├── jupyter │ ├── annotation_names.png │ ├── jupyter_notebook.png │ ├── jupyter_notebook2.png │ └── jupyter_notebook_add_cell.png ├── kmers-metapalette.png ├── login1.png ├── login10.png ├── login11.png ├── login12.png ├── login2.png ├── login3.png ├── login4.png ├── login5.png ├── login6.png ├── login7.png ├── login8.png ├── login9.png ├── markdown_tutorial.tar.gz ├── metagen-alt-close.png ├── metagen-alteromonas.png ├── metagen-anvi-open.png ├── metagen-anvi-summarize.png ├── metagen-anvi-tax.png ├── metagen-bac-choppy.png ├── metagen-bac-transposon-A.png ├── metagen-bac-transposon-B.png ├── metagen-bac-transposon.png ├── metagen-bacteroidetes.png ├── metagen-tricho-bin.png ├── metagenomics_overview.png ├── mm10_refgene.2400x2400.jpeg ├── multiqc_report.html ├── other_anvi.png ├── pan_syn.png ├── phylo_syn.png ├── quast_output.png ├── report.html ├── rmarkdown │ ├── Rmd_output.png │ ├── Rmd_workflow.png │ ├── add_file.png │ ├── chunk_options.png │ ├── create_rmd.png │ ├── insert_code_chunk.png │ ├── knit.png │ ├── knit_button.png │ ├── label_navigation.png │ ├── load_rmd_packages.png │ ├── new_rmd_title.png │ ├── new_rmd_yaml.png │ ├── output_to_viewpane.png │ ├── pop_up_window.png │ ├── publish.png │ ├── republish.png │ ├── rmd_workflow_cheatsheet.png │ └── save_file.png ├── rna-seq-workflow.png ├── rnaseq_samples.csv ├── rstudio-terminal.png ├── sam_file.png ├── schurch_comp.matrix.png ├── shell_example_gene_annots.png ├── shell_tut_file_browser_notes.png ├── shell_tut_jupyter_initial_launch.png ├── shell_tut_jupyter_terminal.png ├── smake_rule.png ├── soft_prob.png ├── sra1.png ├── sra2.png ├── sra3.png ├── sra4.png ├── ssh.png ├── taxonomy1.png ├── taxonomy2.png ├── terminal-nano-2.png ├── terminal-nano.png ├── tmp.txt ├── unix_file_system_structure.png ├── variant_calling_workflow.png ├── wms_rationale.png ├── wms_syntax.png └── workflow_steps.png ├── amplicon_and_metagen.md ├── bash_automation.md ├── chip-seq.md ├── cloud_computing_intro.md ├── cloud_resources.md ├── code-of-conduct.md ├── conda_tutorial.md ├── conf.py ├── dammit_annotation.md ├── de-novo-genome-assembly.md ├── de-novo-genome-exploration.md ├── diff-ex-and-viz.md ├── feel-free-to-reach-out.md ├── finding_resources_online.md ├── github.md ├── guidelines-expectations.md ├── hackmd_notes.md ├── index.md ├── jetstream-bioconda-config.md ├── jetstream ├── boot.md ├── images │ ├── Bears_Project.png │ ├── DIBSI2018_image.png │ ├── DIBSI2018_launch.png │ ├── DIBSI2018_launch.thumb.png │ ├── Image_Search.png │ ├── Image_Search.thumb.png │ ├── Images.png │ ├── Images.thumb.png │ ├── Instance_Active.png │ ├── Instance_Deploying.png │ ├── Instance_Initializing.png │ ├── Instance_WebShell.png │ ├── Instances_Volumes.png │ ├── Launch_Instance.png │ ├── Launch_Instance.thumb.png │ ├── Lisa_Project.png │ ├── delete-1.png │ ├── delete-2.png │ ├── delete-3.png │ ├── delete-4.png │ ├── ec2-moba-2.png │ ├── ec2-moba-3.png │ ├── ec2-moba-4.png │ ├── ip-address.png │ ├── jet_actions.png │ ├── jet_dashboard.png │ ├── jet_links.png │ ├── jet_webshell.png │ ├── jetstream_login.png │ ├── login-1.png │ ├── login-1.thumb.png │ ├── login-10.png │ ├── login-10.thumb.png │ ├── login-11.png │ ├── login-11.thumb.png │ ├── login-12.png │ ├── login-12.thumb.png │ ├── login-2.png │ ├── login-2.thumb.png │ ├── login-3.png │ ├── login-3.thumb.png │ ├── login-4.png │ ├── login-4.thumb.png │ ├── login-5.png │ ├── login-5.thumb.png │ ├── login-6.png │ ├── login-6.thumb.png │ ├── login-7.png │ ├── login-7.thumb.png │ ├── login-8.png │ ├── login-8.thumb.png │ ├── login-9.png │ ├── login-9.thumb.png │ ├── login1.png │ ├── login10.png │ ├── login11.png │ ├── login12.png │ ├── login2.png │ ├── login3.png │ ├── login4.png │ ├── login5.png │ ├── login6.png │ ├── login7.png │ ├── login8.png │ ├── login9.png │ ├── moba-1.png │ ├── password-change.png │ ├── possible_instance_problem.png │ ├── possible_instance_problem.thumb.png │ ├── resume-1.png │ ├── resume-2.png │ ├── resume-3.png │ ├── rstudio.png │ ├── ssh.png │ ├── start-1.png │ ├── start-2.png │ ├── start-3.png │ ├── stop-1.png │ ├── stop-2.png │ ├── stop-3.png │ ├── stop-4.png │ ├── suspend-1.png │ └── suspend-2.png ├── login.md └── ssh_changepassword.md ├── mapping-variant-calling.md ├── more-unix-fun.md ├── online-tools.md ├── quality-and-trimming.md ├── recovering-rep-genomes-from-mgs.md ├── requirements.txt ├── rmarkdown_rnaseq.md ├── running-command-line-blast.md ├── salmon-quant.md ├── scripts ├── gather-counts.py ├── install-edgeR.R └── yeast.salmon.R ├── shell_intro ├── index.md ├── shell-for-loops-05.md ├── shell-getting-started-01.md ├── shell-six-glorious-commands-04.md ├── shell-wild-redirectors-03.md └── shell-working-02.md ├── snakemake_for_automation.md ├── snakemake_for_qc.md ├── sourmash.md ├── toc.rst ├── transcriptome-assembly-nematostella.md ├── transcriptome-assembly.md ├── visualizing-blast-scores-with-RStudio.md └── where_to_put_data.md /.TOUCH: -------------------------------------------------------------------------------- 1 | test 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