Syllabus

January 10: Class Overview and resources.

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

Lecture slides: Introduction lecture slides

January 12: Download needed software

See Resources tab in wiki for things to download for next class.

Class discussion of student current projects, learning goals and objectives.

January 14: Encode history and access

Encode Historical overview Lecture Video

Lecture Slides

Part II: Exploring Encode Portal Video

January 17: No class MLK day

January 19: #!bin_bash_in_data

Video run through of 02_bash_in_data

January 21: Welcome to FIJI lecture by Matt

JPart I: Historical overview of ENCODE Video

-*- 01_encode.Rmd

-*- 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.

*** Please read these papers for February 19th class ***

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

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

Paper from last years class !

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 & Journal club

February 22: Explore larger pre-cooked data set

Video overview of 08_R_functions_consensus_peaks

-*- 08_R_functions_consensus_peaks

February 24: ExploRing the data in R part I.

Video overview of 09_1_Iranges_Granges_intro.Rmd

-*- 09_1_Iranges_Granges_intro.Rmd

Video overview of 09_2_Genomic_features_as_ranges.Rmd

-*- 09_2_Genomic_features_as_ranges.Rmd

February 26: Exploring Data in R part II

Video overview of 10_Ranges.Rmd

-*- 10_our_data_ranges.Rmd

March 1: Regroup and Finish 10

March 3: What exactly are all of these DBPs?

Class video DNA binding proteins, their motifs and meta-properties

Class slides

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

March 5: Plotting in R part I.

Video overview of 11_plotting.Rmd

-*- 11_plotting.Rmd

March 8: ExploRing Data in R part III.

video overview of global clustering

-*- 12_Global_clustering_analyses.Rmd

March 10: ExploRing Data in R part IV : getting meta with promoter profile plots

video overview of promoter binding profile meta plots

-*- 13_promoter_binding_meta_plots.Rmd

March 12: Intuitive Statistics

Video overview of intuitive statistical principles

SLides for Intuitive Statistics

March 15: Intro to RNAseq

[Video overview Intro to RNAseq Pipeline].()

-*- [14_intro_rnaseq.Rmd].()

March 17: RNAseq part II

[Video overview Analyzing RNAseq].()

-*- [15_rnaseq_for_real.Rmd].()

March 19: Differential expression of CRISPR WT vs KO.

[Video overview differential expression].() -*- 16_differential_expression.Rmd

March 22: Binding versus Expression

[Video overview binding versus Expression].()

-*- 17_binding_vs_expression.Rmd

March 24: ExploRing Repeat Features

-*- 15_repeats.Rmd

March 26: wellness day 2 (for this class)

March 29: Defining reservoirs

-*- 16_reservoirs.Rmd

March 31: Reservoir binding properties

-*- 17_resevoir_properties.Rmd

April 2: Reservoir comparison to k562

-*- 18_resevoir_compare.Rmd

April 5: Reservoir Nascent RNA

-*- 19_resevoir_ProSeq.Rmd

April 7: Reservoir Chromatin

-*- 20_resevoir_chromatin.Rmd

April 9: Class regroup data presentations -- further analyses --

April 12: Visualization [lecture ]

• outline figures for paper.

April 14: Analysis and figures I

-*- .RMD FREESTYLE

April 16: Analysis and figures II

-*- .RMD FREESTYLE

April 19: Analysis and figures III

-*- .RMD FREESTYLE

April 21: Paper writing [ lecture ]

-start writing paper with current results

April 23: Put paper together I

April 26: Put paper together II

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

END