Last updated: 2020-04-03
Checks: 2 0
Knit directory: Comparative_APA/analysis/
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| Rmd | 767bb78 | brimittleman | 2020-04-03 | update anno |
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| Rmd | 164c237 | brimittleman | 2020-03-16 | ask about anno bias |
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| Rmd | 6f7dfd7 | brimittleman | 2020-03-14 | add basecomp analysis |
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| Rmd | 2e8ed44 | brimittleman | 2020-02-21 | add Splice site strength |
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| Rmd | 86aabf2 | brimittleman | 2020-01-28 | add expression overlap with APA exploration |
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| Rmd | a018c33 | brimittleman | 2020-01-23 | add diff usgage and ss |
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| Rmd | 908f02d | brimittleman | 2020-01-23 | add compare filter and write out for top SS |
| html | 8a24b59 | brimittleman | 2020-01-22 | Build site. |
| Rmd | 97ef45e | brimittleman | 2020-01-22 | add mediation DF |
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| Rmd | d886866 | brimittleman | 2020-01-22 | add correlation between pheno DF |
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| Rmd | 07fd459 | brimittleman | 2020-01-22 | DF for upset and translation protein ven |
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| Rmd | 117fd63 | brimittleman | 2020-01-21 | redo differential analysis with double filt |
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| Rmd | 46c489b | brimittleman | 2020-01-21 | nuclear diff filtered |
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| Rmd | 010c249 | brimittleman | 2020-01-21 | DF species specific |
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| Rmd | 414b47c | brimittleman | 2020-01-21 | update dominant PAS |
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| 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 |
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| 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 |
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| 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 |
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| Rmd | 1121102 | brimittleman | 2020-01-13 | add dpau and de overlap with dom intronic |
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| Rmd | 928a30d | brimittleman | 2020-01-09 | add same and diff dom ss analysis |
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| Rmd | 1cdc21d | brimittleman | 2020-01-09 | add initial signal site analysis |
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| 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 | 2019-11-23 | Build site. |
| Rmd | c48aedc | brimittleman | 2019-11-23 | 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 | 2019-11-19 | Build site. |
| Rmd | 7c206f8 | brimittleman | 2019-11-19 | add extra QC anaylsis |
| html | 9ecd769 | brimittleman | 2019-11-19 | Build site. |
| Rmd | db85b26 | brimittleman | 2019-11-19 | 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 | 2019-10-01 | Build site. |
| Rmd | b5a2151 | brimittleman | 2019-10-01 | 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.
List of everything we tried for this section:
Liftover
Annotate and make phenotype
Evaluate results:
From before reseq:
From the original nuclear dominant