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Last updated: 2019-12-08

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Knit directory: Comparative_APA/analysis/

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    Untracked:  data/cleanPeaks_lifted/
    Untracked:  data/liftover_files/
    Untracked:  data/metadata_HCpanel.txt
    Untracked:  data/metadata_HCpanel.xlsx
    Untracked:  data/primaryLift/
    Untracked:  data/reverseLift/
    Untracked:  data/~$RNASEQ_metadata.xlsx
    Untracked:  data/~$metadata_HCpanel.xlsx
    Untracked:  data/.xlsx
    Untracked:  output/dtPlots/
    Untracked:  projectNotes.Rmd

Unstaged changes:
    Modified:   analysis/CorrbetweenInd.Rmd
    Modified:   analysis/PASnumperSpecies.Rmd
    Modified:   analysis/annotatePAS.Rmd
    Modified:   analysis/annotationInfo.Rmd
    Modified:   analysis/diffSplicing.Rmd
    Modified:   analysis/liftoverPAS.Rmd
    Modified:   analysis/multiMap.Rmd
    Modified:   analysis/verifyBAM.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File	Version	Author	Date	Message
Rmd	f04a804	brimittleman	2019-12-08	add DE vs DS analysis
html	b32d961	brimittleman	2019-12-05	Build site.
Rmd	1452408	brimittleman	2019-12-05	add investigation pantro5
html	144bc43	brimittleman	2019-12-05	Build site.
Rmd	d56d98c	brimittleman	2019-12-05	add opp map
html	f53ab27	brimittleman	2019-11-24	Build site.
Rmd	c48aedc	brimittleman	2019-11-24	add multimap stat graphs
html	e7cb428	brimittleman	2019-11-21	Build site.
Rmd	9fbd1fe	brimittleman	2019-11-21	figure out sample swap
html	2e33ce9	brimittleman	2019-11-21	Build site.
Rmd	17d5d33	brimittleman	2019-11-21	add diff splice without 2 samples
html	40db68c	brimittleman	2019-11-20	Build site.
Rmd	7c206f8	brimittleman	2019-11-20	add extra QC anaylsis
html	9ecd769	brimittleman	2019-11-20	Build site.
Rmd	db85b26	brimittleman	2019-11-20	add remove 2 analysis
html	dc91b0a	brimittleman	2019-11-11	Build site.
Rmd	b5ba82e	brimittleman	2019-11-11	add diff expression and diff splicing
html	066d419	brimittleman	2019-10-16	Build site.
Rmd	a255e22	brimittleman	2019-10-16	add code and annotations for dt plots
html	f4bcae9	brimittleman	2019-10-15	Build site.
Rmd	25a8b1e	brimittleman	2019-10-15	fix name bug add number PAS analysis
html	d9f241f	brimittleman	2019-10-11	Build site.
Rmd	36d8ded	brimittleman	2019-10-11	add correlation between ind analysis
html	3f3c4d0	brimittleman	2019-10-10	Build site.
Rmd	c4db4f0	brimittleman	2019-10-10	add non norm pca and verify bam
html	b8ccfdb	brimittleman	2019-10-09	Build site.
Rmd	1f06329	brimittleman	2019-10-09	add PCA by total and nuclear
html	d0c98c2	brimittleman	2019-10-09	Build site.
Rmd	14a3f66	brimittleman	2019-10-09	add pca and human v chimp in nuc analysis
html	c3aa529	brimittleman	2019-10-07	Build site.
Rmd	da85ad8	brimittleman	2019-10-07	add code to prepare human and chimp TvN
html	4ea2576	brimittleman	2019-10-04	Build site.
Rmd	920abac	brimittleman	2019-10-04	add comaprison to old PAS
html	e0ac227	brimittleman	2019-10-03	Build site.
Rmd	e3f0cdf	brimittleman	2019-10-03	add annotation analysis
html	b5edd8e	brimittleman	2019-10-02	Build site.
Rmd	b5a2151	brimittleman	2019-10-02	add analysis for liftover
html	0e8aa0d	brimittleman	2019-10-01	Build site.
Rmd	7d81da8	brimittleman	2019-10-01	add map stats to site
html	7a9cf74	brimittleman	2019-09-24	Build site.
Rmd	a2fe9d6	brimittleman	2019-09-24	add annotation prep anaylsis
html	03cb9ab	brimittleman	2019-09-02	Build site.
html	88ed6b4	brimittleman	2019-09-02	Build site.
Rmd	b6db8f3	brimittleman	2019-09-02	add project info to about and index
html	d03d7b0	brimittleman	2019-09-02	Build site.
Rmd	f914d49	brimittleman	2019-09-02	Start workflowr project.

I am interesting in understanding differential APA between human and chimpanzees. I used 3’ Seq to identify PAS for total and nuclear frations of LCL in both species.