Last updated: 2020-03-09
Checks: 2 0
Knit directory: Comparative_APA/analysis/
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| Rmd | 552842c | brimittleman | 2020-03-09 | add TvN |
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| Rmd | 680d435 | brimittleman | 2020-03-06 | add ptm analysis |
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| Rmd | 86aabf2 | brimittleman | 2020-01-28 | add expression overlap with APA exploration |
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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 |
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| Rmd | e1c6d25 | brimittleman | 2020-01-14 | add analysis on species spec PAS |
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| 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 |
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| Rmd | 6e3027a | brimittleman | 2020-01-07 | upset plots for comparisons |
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| Rmd | 670020f | brimittleman | 2020-01-07 | add translation protien overlap |
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| Rmd | 54015c8 | brimittleman | 2020-01-06 | add overlap dom with dAPA |
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| 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 |
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| Rmd | 5b25363 | brimittleman | 2019-12-30 | add total and nuclear dominant PAS analysis |
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| 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 |
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| Rmd | de41e07 | brimittleman | 2019-12-16 | add gene comp 5v6 |
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| Rmd | 3b64d8c | brimittleman | 2019-12-16 | add compare ortho exon |
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| Rmd | 8068598 | brimittleman | 2019-12-12 | meta data by species |
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| Rmd | f04a804 | brimittleman | 2019-12-08 | add DE vs DS analysis |
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| Rmd | 1452408 | brimittleman | 2019-12-05 | add investigation pantro5 |
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| Rmd | d56d98c | brimittleman | 2019-12-05 | add opp map |
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| Rmd | c48aedc | brimittleman | 2019-11-23 | add multimap stat graphs |
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| Rmd | 9fbd1fe | brimittleman | 2019-11-21 | figure out sample swap |
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| Rmd | 17d5d33 | brimittleman | 2019-11-21 | add diff splice without 2 samples |
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| Rmd | 25a8b1e | brimittleman | 2019-10-15 | fix name bug add number PAS analysis |
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| Rmd | 36d8ded | brimittleman | 2019-10-11 | add correlation between ind analysis |
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| Rmd | c4db4f0 | brimittleman | 2019-10-10 | add non norm pca and verify bam |
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| Rmd | 1f06329 | brimittleman | 2019-10-09 | add PCA by total and nuclear |
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| Rmd | 14a3f66 | brimittleman | 2019-10-09 | add pca and human v chimp in nuc analysis |
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| Rmd | da85ad8 | brimittleman | 2019-10-07 | add code to prepare human and chimp TvN |
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| Rmd | 920abac | brimittleman | 2019-10-04 | add comaprison to old PAS |
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| Rmd | e3f0cdf | brimittleman | 2019-10-03 | add annotation analysis |
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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 here on, I did everything double filtered:
From here on, I did everything double filtered:
Explore more about APA expression relationship with overlaping significant genes
Apa and expression relationship for seperated by location of PAS
Look at genes that have differences in protein levels and APA levels but not mRNA expression
From before reseq:
From the original nuclear dominant