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 [ lecture ] . ()

January 25: Encode history and access

Historical overview of ENCODE Video Encode Lecture Video

Historical overview of ENCODE slides Lecture Slides

Exploring Encode Portal Video Exploring Encode Portal Video

Let's download data from ENCODE portal! 01_endode.Rmd Video

Link to 01_endode.Rmd file

-*- 01_encode.Rmd

January 27: #!bin/bashing data

-*- 02_bashing_data.Rmd

January 29: Git, got it good!

-*- 03_git.Rmd

February 1: Zhiping ENCODE guest lecture

February 3: Fiji-viz R Studio

-*- 04_R-eading_in_files.Rmd

February 5: Creating a design file -- bashing R.

-*- 05_design_file.Rmd

February 8: Flowing forward with Nextflow [ lecture ]

-install nextflow

February 10: Nextflow set up, slurm and run!

-*- 06_nextflow.Rmd

February 12: Looking under the hood of Nextflow [ lecture ]

• debugging nextflow run

February 15: Visualization of Data

• Igv, UCSC file formats.

February 17: Wellness Day

February 19: Student presentations of data

February 22: Explore larger pre-cooked data set

February 24: Iranges and Granges

-*- 07_Granges.Rmd

February 26: From DNA protein structure to meta-analyses [ Lecture ]

-brainstorm analyses students are interested in performing.

March 1: ExploRing Data in R part I (Defining Consensus Peaks)

-*- 08_consensus_peaks.Rmd

March 3: Plotting in R part I.

-*- 09_plotting.Rmd

ExploRing Data in R part II -*- 10_intersecting_features_peak_characteristics.Rmd

March 5: Intuitive statistical principles [ Lecture ]

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

-*- 11_statistical_significance_of_feature_overlaps.Rmd -read Class, Mele and Kelley papers

March 12: Applying statistics to our data set part II (lncRNA -vs- mRNA promoters).

-*- 12_permuations_fisher_exact.Rmd

March 15: Class Paper discussion and outline.

-Class, Mele and Kelley et al paper discussion.

March 17: Plotting in R part II.

-*- 13_plotting.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