Last updated: 2020-01-21
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Knit directory: Comparative_APA/analysis/
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Unstaged changes:
Modified: analysis/OppositeMap.Rmd
Modified: analysis/annotationInfo.Rmd
Modified: analysis/comp2apaQTLPAS.Rmd
Modified: analysis/correlationPhenos.Rmd
Modified: analysis/establishCutoffs.Rmd
Modified: analysis/investigatePantro5.Rmd
Modified: analysis/multiMap.Rmd
Modified: analysis/speciesSpecific.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 | 010c249 | brimittleman | 2020-01-21 | DF species specific |
| html | 48db342 | brimittleman | 2020-01-21 | Build site. |
| Rmd | 414b47c | brimittleman | 2020-01-21 | update dominant PAS |
| html | 5525b39 | brimittleman | 2020-01-21 | Build site. |
| Rmd | 2e66af9 | brimittleman | 2020-01-21 | add ss and PAS num DF |
| html | 80f647a | brimittleman | 2020-01-19 | Build site. |
| Rmd | 96b46ba | brimittleman | 2020-01-19 | add enrichment in apapQTLs |
| html | c211e21 | brimittleman | 2020-01-18 | Build site. |
| Rmd | 7a9f608 | brimittleman | 2020-01-18 | finished benchmark |
| html | 5eef3eb | brimittleman | 2020-01-16 | Build site. |
| Rmd | 5c24c0c | brimittleman | 2020-01-16 | add cutoff code files |
| html | 7e3ab25 | brimittleman | 2020-01-16 | Build site. |
| Rmd | c0b3ef6 | brimittleman | 2020-01-16 | add correlation between pheons |
| html | 0a3545a | brimittleman | 2020-01-15 | Build site. |
| Rmd | 5dd5e35 | brimittleman | 2020-01-15 | add code to viz nuclear dapa |
| html | 4f5d492 | brimittleman | 2020-01-14 | Build site. |
| Rmd | 3cce3da | brimittleman | 2020-01-14 | start mediation analysis |
| html | c74c3df | brimittleman | 2020-01-14 | Build site. |
| Rmd | e1c6d25 | brimittleman | 2020-01-14 | add analysis on species spec PAS |
| html | 1b9ae04 | brimittleman | 2020-01-13 | Build site. |
| Rmd | 5ea4710 | brimittleman | 2020-01-13 | add questions about dAPA pas and genes |
| html | b963392 | brimittleman | 2020-01-13 | Build site. |
| Rmd | 1121102 | brimittleman | 2020-01-13 | add dpau and de overlap with dom intronic |
| html | df07f1a | brimittleman | 2020-01-09 | Build site. |
| Rmd | 928a30d | brimittleman | 2020-01-09 | add same and diff dom ss analysis |
| html | ced1966 | brimittleman | 2020-01-09 | Build site. |
| Rmd | 1cdc21d | brimittleman | 2020-01-09 | add initial signal site analysis |
| html | dd02dab | brimittleman | 2020-01-09 | Build site. |
| html | a41141b | brimittleman | 2020-01-09 | Build site. |
| Rmd | 93ced1e | brimittleman | 2020-01-09 | peak 2 pas |
| html | 6d9e369 | brimittleman | 2020-01-08 | Build site. |
| Rmd | 203eae5 | brimittleman | 2020-01-08 | first steps for intron loc analysis |
| html | 4c87e96 | brimittleman | 2020-01-07 | Build site. |
| Rmd | 6e3027a | brimittleman | 2020-01-07 | upset plots for comparisons |
| html | 7768535 | brimittleman | 2020-01-07 | Build site. |
| Rmd | 670020f | brimittleman | 2020-01-07 | add translation protien overlap |
| html | dec23c1 | brimittleman | 2020-01-06 | Build site. |
| Rmd | 54015c8 | brimittleman | 2020-01-06 | add overlap dom with dAPA |
| html | c633e63 | brimittleman | 2020-01-06 | Build site. |
| Rmd | 5e85704 | brimittleman | 2020-01-06 | add overlap with eQTLs |
| html | dc41b3b | brimittleman | 2019-12-30 | Build site. |
| Rmd | 6214ec5 | brimittleman | 2019-12-30 | add venn diagram for diff apa |
| html | 42a8b12 | brimittleman | 2019-12-30 | Build site. |
| Rmd | 385057f | brimittleman | 2019-12-30 | fix dom PAS on index |
| html | 0176b49 | brimittleman | 2019-12-30 | Build site. |
| Rmd | 5b25363 | brimittleman | 2019-12-30 | add total and nuclear dominant PAS analysis |
| html | 2644747 | brimittleman | 2019-12-27 | Build site. |
| Rmd | 4c8973d | brimittleman | 2019-12-27 | add total human vs chimp |
| html | ffecde8 | brimittleman | 2019-12-17 | Build site. |
| Rmd | d541bb5 | brimittleman | 2019-12-17 | move extra pcas |
| html | 8b074b8 | brimittleman | 2019-12-16 | Build site. |
| 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.
From before reseq:
From the original nuclear dominant