Last updated: 2018-07-19

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Expand here to see past versions:

File	Version	Author	Date	Message
Rmd	0d7956a	Briana Mittleman	2018-07-19	add smash analysis
html	fb4fdaa	Briana Mittleman	2018-07-03	Build site.
Rmd	9e3b286	Briana Mittleman	2018-07-03	fix net4
html	bfeb0fb	Briana Mittleman	2018-07-03	Build site.
html	363ea13	Briana Mittleman	2018-06-22	Build site.
Rmd	97a0c53	Briana Mittleman	2018-06-22	wflow_publish(c(“analysis/index.Rmd”, “analysis/net-4-explore.Rmd”))
html	d76f54d	Briana Mittleman	2018-04-05	Build site.
Rmd	c269f0f	Briana Mittleman	2018-04-05	fixr eqtl by strand bullet
html	465e616	Briana Mittleman	2018-04-03	Build site.
html	0a0b388	Briana Mittleman	2018-03-22	Build site.
Rmd	0e50352	Briana Mittleman	2018-03-22	start strand specific analysis
html	09e78cf	Briana Mittleman	2018-03-19	Build site.
Rmd	3aa98a8	Briana Mittleman	2018-03-19	add recreate rmd to index
html	fd42b70	Briana Mittleman	2018-03-16	Build site.
Rmd	1707538	Briana Mittleman	2018-03-16	initialize growth analysis
html	b789dd9	Briana Mittleman	2018-03-02	Build site.
Rmd	646ee57	Briana Mittleman	2018-03-02	initialize analysis for the pilot data
html	a84f24a	Briana Mittleman	2018-02-14	Build site.
html	d72c447	Briana Mittleman	2018-02-02	Build site.
Rmd	01f846f	Briana Mittleman	2018-02-02	wflow_publish(c(“index.Rmd”, “use_deeptools.Rmd”))
html	558ff5a	Briana Mittleman	2018-01-31	Build site.
Rmd	308d2b5	Briana Mittleman	2018-01-31	add utr cov to index
html	2f36a96	Briana Mittleman	2018-01-25	Build site.
Rmd	52df489	Briana Mittleman	2018-01-25	stranded graphs and add to index
html	8a554c1	Briana Mittleman	2017-12-13	Build site.
Rmd	3ed7074	Briana Mittleman	2017-12-13	create plots for actb and add to index
html	3326147	Briana Mittleman	2017-12-08	Build site.
Rmd	fab79ca	Briana Mittleman	2017-12-08	reforat gene count data for ggplot
html	f006037	Briana Mittleman	2017-11-30	Build site.
Rmd	b180d9a	Briana Mittleman	2017-11-30	fix index formating
html	ec2d994	Briana Mittleman	2017-11-30	Build site.
Rmd	35b1aa1	Briana Mittleman	2017-11-30	wflow_publish(c(“bin_windows.Rmd”, “index.Rmd”, “reads_in_genes.Rmd”))
html	552910d	Briana Mittleman	2017-11-28	Build site.
Rmd	7041a54	Briana Mittleman	2017-11-28	add reads_in_gene
html	697f6a0	Briana Mittleman	2017-11-20	Build site.
Rmd	560df7d	Briana Mittleman	2017-11-20	initiate the reads in gene analysis and add it to index
html	121c3e0	Briana Mittleman	2017-11-16	Build site.
Rmd	acd27cd	Briana Mittleman	2017-11-16	add map_stats to inde
html	3d6ebfe	Briana Mittleman	2017-11-09	Build site.
Rmd	aee8225	Briana Mittleman	2017-11-09	initialize and load data for genomation data
html	1d36dec	Briana Mittleman	2017-11-08	Build site.
Rmd	9a86ba3	Briana Mittleman	2017-11-08	Initiate the explore UMI usage analysis
html	4207b60	Briana Mittleman	2017-11-06	Build site.
Rmd	7eeb4e1	Briana Mittleman	2017-11-06	start initial data exploration and add it to index
Rmd	baeec88	Briana Mittleman	2017-10-26	commit index and config changes
html	5096c14	Briana Mittleman	2017-10-26	Build site.
Rmd	4c45592	Briana Mittleman	2017-10-26	add new config/snake file to index
html	0ea88cc	Briana Mittleman	2017-10-24	Build site.
Rmd	13f7b6a	Briana Mittleman	2017-10-24	move conda code to conda environment analysis and update
html	5f7df97	Briana Mittleman	2017-10-24	Build site.
Rmd	f03ffb4	Briana Mittleman	2017-10-17	add test analysis
html	e445d99	Briana Mittleman	2017-10-17	Build site.
html	6ee857d	Briana Mittleman	2017-10-17	Build site.
Rmd	c88cd2e	Briana Mittleman	2017-10-17	Publish the initial files for myproject
Rmd	d639248	Briana Mittleman	2017-10-17	Start workflowr project.

---

This is the workflowr site for my Net-seq project. I will have all of the data, code, and analysis here.

Set-up for mappping my libraries:

• Setting up conda environment

• Setting up config and snake files

Initial data exploration:

• Initial data exploration for NetSeq1 libary

• Explore read lengths that are mapping

• Explore the UMI usage in the NetSeq1 library

• Use the genomation package to vizualize genome features and see overlap with Net-seq1

• Exploration of read counts per gene

• Reformat gene counts for ggplot2 data analysis

• Explore read counts per genome bin

• Create IGV browser style plots

Initial analysis for Net-3:

• Net-3 Initial exploration

Net-pilot analysis:

• Update snakefile for pilot analysis

• Create blacklist to filter reads

• Recreate figures from Mayer

• Strand specific analysis

• Connect eQTLs to strand

Cell Growth analysis:

• Initial plots on growth

Exploration of the 3` seq and ApA sites:

• Look for read enrichment at ApA sites

• UTR coverage analysis

• Look at enrichment using Deep tools

Net 4 analysis- includes 3 lanes for all 16 individuals:

• Explore Net 4

Smoothing data:

• Test smash on netseq 3 first 8 ind.

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This reproducible R Markdown analysis was created with workflowr 1.0.1

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