Last updated: 2020-03-17
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Knit directory: Comparative_APA/analysis/
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Unstaged changes:
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| Rmd | bec8ae9 | brimittleman | 2020-03-17 | add mis filter annotation and pheno |
| html | 45bfe96 | brimittleman | 2020-03-17 | Build site. |
| Rmd | c4282a6 | brimittleman | 2020-03-17 | add change filter lifts |
| html | 86238eb | brimittleman | 2020-03-16 | Build site. |
| Rmd | 164c237 | brimittleman | 2020-03-16 | ask about anno bias |
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| Rmd | 94211e8 | brimittleman | 2020-03-16 | add change misprime analysis and dapa qtls |
| html | 3bcfc08 | brimittleman | 2020-03-14 | Build site. |
| Rmd | 6f7dfd7 | brimittleman | 2020-03-14 | add basecomp analysis |
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| Rmd | 0445720 | brimittleman | 2020-03-13 | add map stats when you remove Ns |
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| Rmd | 552842c | brimittleman | 2020-03-09 | add TvN |
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| Rmd | c6a11f0 | brimittleman | 2020-03-07 | add expression indep |
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| Rmd | 680d435 | brimittleman | 2020-03-06 | add ptm analysis |
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| Rmd | ad95271 | brimittleman | 2020-03-04 | add upstream control |
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| Rmd | 7385496 | brimittleman | 2020-02-24 | add correlations plotted by location |
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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 | 1673f18 | brimittleman | 2020-01-23 | start the prot mediation cant do diff indiv |
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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 |
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| 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 |
| html | df07f1a | brimittleman | 2020-01-09 | Build site. |
| 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 |
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| 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 |
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| 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 |
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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 |
| 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 |
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| Rmd | b5a2151 | brimittleman | 2019-10-01 | add analysis for liftover |
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| Rmd | 7d81da8 | brimittleman | 2019-10-01 | add map stats to site |
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| Rmd | a2fe9d6 | brimittleman | 2019-09-24 | add annotation prep anaylsis |
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| Rmd | b6db8f3 | brimittleman | 2019-09-02 | add project info to about and index |
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| 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 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
Liftover
Annotate and make phenotype
From before reseq:
From the original nuclear dominant