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_install_$PATH_trial-design.Rmd

-*- 05_nextflow_install_$PATH_trial-design.Rmd

February 8: Fresh Nextflow Run for your favorite DBP.

Choose your own ChIP adventure. Use class above and the .Rmd file below to do a new run of your favorite protein!

-*- 06_run.sh_exeRcise.Rmd

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

VIDEO: Exploring the Pipeline and output files

SLIDES: Exploring the Pipeline and output files

Video IGV Visualization of NF-Core ChiPseq output files

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 overview of 08_R_functions_consensus_peaks]. (JR - Done)

-*- 08_R_functions_consensus_peaks

February 24: ExploRing the data in R part I.

[Video overview of 09_1_Iranges_Granges_intro.Rmd] . (JR)

-*- 09_1_Iranges_Granges_intro.Rmd

[Video overview of 09_2_Genomic_features_as_ranges.Rmd] . (JR)

-*- 09_2_Genomic_features_as_ranges.Rmd

*** Please read these papers for March 3rd class ***

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

February 26: Exploring Data in R part II

[Video overview of 10_Ranges.Rmd]. (JR)

-*- 10_our_data_ranges.Rmd

March 1: What exactly are all of these DBPs?

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

[Class slides].()

Class discussion of Mele and Kelley papers above as spring board to brainstorm analyses for class -- and get used to Meta analyses.

March 3: Plotting in R part I.

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

-*- 11_plotting.Rmd

March 5: ExploRing Data in R part III.

[video overview 12]. (JR)

-*- 12_Global_analyses.Rmd -clustering etc

March 8: ExploRing Data in R part IV : getting meta

[video overview 13]. (MS)

-*- 13_meta_plots.Rmd

• promoter profile plots

March 12: Intuitive statistical principles

[Video overview of intuitive statistical principles].(JR)

[SLides:].(Video overview of intuitive statistical principles)

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

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 ]. ()

[Video overview RNAseq_basics.Rmd] .() -*- 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