Syllabus

January 15: Class Overview and resources.

Course Introduction, overview and inquiry based objectives: Introduction lecture Video

Lecture slides: Introduction lecture slides

January 18: MLK day

January 20: See Resources tab in wiki for things to download for next lecture. Class discussion of student current projects, learning goals and objectives.

January 22: [Welcome to FIJI lecture by Jon and Matt].()

January 25: Encode history and access

Part I: Historical overview of ENCODE Video

Encode Historical overview Lecture Video

Lecture Slides

Part II: Exploring Encode Portal Video

Part III: Let's download data from ENCODE portal!

Video run through of 01_endode.Rmd

-*- 01_encode.Rmd

January 27: #!bin_bash_in_data

Video run through of 02_bash_in_data

-*- 02_bash_in_data.Rmd

January 29: Git, got it, good!

What is git bash and git bash background

Video introduction to git

presentation slides

Video run through of 03_get_git.Rmd

-*- 03_get_git.Rmd

February 1: Zhiping ENCODE guest lecture

February 3: Fiji-viz R Studio

Download VPN to connect with fiji-viz -- and instructions

link to Fiji R-viz

-- https://fiji-viz.colorado.edu/

Video overview of R-viz / R-Studio > install.packages

[Video introduction to R].()

[Slides introduction to R].()

-*- data files for today's class ~ 1.3Gb

--- place these files in /Shares/rinn_class/data/CLASS_2021/students/data

Video run through of 04_R-eading_in_files.Rmd

-*- 04_R-eading_in_files.Rmd

February 5: Flowing forward with Nextflow

[Video introduction to Nextflow].()

[Slides introduction to Nextflow].()

[video overview of 05_nextflow_.Rmd].()

-*- 05_nextflow_install_$PATH_trial-design.Rmd

February 8: Fresh Nextflow Run for your favorite DBP.

-*- 06_nextflow_run.sh.Rmd

February 10: Exploring and visualization of NF-CORE Chipseq pipeline.

[VIDEO: Exploring and visualization of NF-CORE_Chipseq output files] . ()

SLIDES: Exploring the Pipeline and output files

[Video IGV Visualization of NF-Core ChiPseq pipeline].()

February 12: Visualizing, debugging, exploring new run results.

February 15: Exploring the data more in UCSC

[Video overview of UCSC Genome Browser - basics to custom tracks] . ()

-*- 07_UCSC_formating.Rmd

February 17: Wellness Day

February 19: Student presentations of data

February 22: Explore larger pre-cooked data set

[Video introduction toRanges, Iranges and Granges] . (MS)

[Slides introduction toRanges, Iranges and Granges] . (MS)

[Video overview of 08]. (JR) -*- [08_R_functions_consensus_peaks]. (JR)

February 24: ExploRing the data in R part I.

[Video overview of 09]. (JR) -*- 09_genomic_peak_properties.

• general characterization and clustering.

February 26:

[ Class video DNA binding proteins, their motifs and meta-properties]. (JR)

[Class slides].()

-brainstorm analyses students are interested in performing.

March 1: ExploRing Data in R part II : getting meta

[video overview 10]. (MS) -*- 10_meta_plots.Rmd

March 3: Plotting in R part I.

[Video overview of 11].(JR) -*- 11_plotting.Rmd

ExploRing Data in R part III [video overview 12]. (JR) -*- 12_intersecting_features_peak_characteristics.Rmd -lncRNA mRNA, expression

March 5: [Intuitive statistical principles].(MS)

-read Class, Mele and Kelley papers

March 8: Applying statistics to our data part I (global clustering, promter_feature_profile_plots)

[overview of 13].(MS) -*- 13_Stats_in_feature_overlaps.Rmd

March 12: Class Paper discussion and outline.

-Class, Mele and Kelley et al paper discussion.

March 15: Plotting in R part II.

-*- 14_practical plots for our studies.Rmd

March 17: RNA sequencing intro and analysis

[Video overview Nextflow RNA Seq & where is the data]. ()

[Slides overview Nextflow RNA Seq & where is the data]. ()

[Video overview RNA seq & Differential Expression ]. ()

[Slides overview RNA seq & Differential Expression ]. ()

-*- 15_RNAseq_basics.Rmd

March 19: Binding versus Expression

-*- 14_binding_vs_expression.Rmd

March 22: ExploRing Repeat Features

-*- 15_repeats.Rmd

March 24: wellness day 2 (for this class)

March 26: Defining reservoirs

-*- 16_reservoirs.Rmd

March 29: Reservoir binding properties

-*- 17_resevoir_properties.Rmd

March 31: Reservoir comparison to k562

-*- 18_resevoir_compare.Rmd

April 2: Reservoir Nascent RNA

-*- 19_resevoir_nascent.Rmd

April 5: Reservoir Chromatin

-*- 20_resevoir_chromatin.Rmd

April 7: Class regroup data presentations -- further analyses --

April 9: Visualization [lecture ]

• outline figures for paper.

April 12: Analysis and figures I

-*- .RMD FREESTYLE

April 14: Analysis and figures II

-*- .RMD FREESTYLE

April 16: Analysis and figures III

-*- .RMD FREESTYLE

April 19: Paper writing [ lecture ]

-start writing paper with current results

April 21: Put paper together I

April 23: Put paper together II

April 26: Put paper together III

April 28: Regroup clean up git and finalize paper plans!

END