Last updated: 2019-12-16
Checks: 2 0
Knit directory: Comparative_APA/analysis/
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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/OppositeMap.Rmd
Modified: analysis/PASnumperSpecies.Rmd
Modified: analysis/annotatePAS.Rmd
Modified: analysis/annotationInfo.Rmd
Modified: analysis/diffExpression.Rmd
Modified: analysis/investigatePantro5.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 | de41e07 | brimittleman | 2019-12-16 | add gene comp 5v6 |
| html | 1b69793 | brimittleman | 2019-12-16 | Build site. |
| Rmd | 3b64d8c | brimittleman | 2019-12-16 | add compare ortho exon |
| html | cbadb32 | brimittleman | 2019-12-12 | Build site. |
| Rmd | 8068598 | brimittleman | 2019-12-12 | meta data by species |
| html | 3ee8382 | brimittleman | 2019-12-08 | Build site. |
| 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.
Preparation and QC:
Catalog PAS:
Differential Isoform Analysis:
Quantify Phenotypes with RNA:
Extra QC and Analysis