Last updated: 2020-05-31
Checks: 2 0
Knit directory: Comparative_APA/analysis/
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Unstaged changes:
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| Rmd | 033290c | brimittleman | 2020-05-31 | add main figures 1-4 |
| html | 24d63d8 | brimittleman | 2020-05-28 | Build site. |
| Rmd | 1cc5ab7 | brimittleman | 2020-05-28 | add total diff |
| html | 957e640 | brimittleman | 2020-05-23 | Build site. |
| Rmd | 34708c2 | brimittleman | 2020-05-23 | check switch genes |
| html | 2d70737 | brimittleman | 2020-05-22 | Build site. |
| Rmd | c5cb2cc | brimittleman | 2020-05-22 | add prot mod and effect sizes |
| html | 88ca1ad | brimittleman | 2020-05-21 | Build site. |
| Rmd | 89a7189 | brimittleman | 2020-05-21 | add fix effect dir and intronic plots |
| html | da8b118 | brimittleman | 2020-05-21 | Build site. |
| Rmd | fd04a01 | brimittleman | 2020-05-21 | add U rich analysis |
| html | 1c9c769 | brimittleman | 2020-05-20 | Build site. |
| Rmd | 66cadcb | brimittleman | 2020-05-20 | biological insight? |
| html | e196e58 | brimittleman | 2020-05-20 | Build site. |
| Rmd | 193632e | brimittleman | 2020-05-20 | add expression levels by dapa and direction |
| html | d35ce8a | brimittleman | 2020-05-18 | Build site. |
| Rmd | ece1103 | brimittleman | 2020-05-18 | add same diff dom and te |
| html | dea6d31 | brimittleman | 2020-05-14 | Build site. |
| Rmd | 2d10282 | brimittleman | 2020-05-14 | add phastcon |
| html | ab6b356 | brimittleman | 2020-05-14 | Build site. |
| Rmd | 3c19233 | brimittleman | 2020-05-14 | add which PAS and seq between |
| html | 1bf3145 | brimittleman | 2020-05-12 | Build site. |
| Rmd | b98f844 | brimittleman | 2020-05-12 | add seq between analysis |
| html | e24f543 | brimittleman | 2020-05-08 | Build site. |
| Rmd | a29b1d2 | brimittleman | 2020-05-08 | add QC double filt |
| html | b418f79 | brimittleman | 2020-05-07 | Build site. |
| Rmd | d13b414 | brimittleman | 2020-05-07 | add dp not de |
| html | 7240370 | brimittleman | 2020-05-07 | Build site. |
| Rmd | 4e19738 | brimittleman | 2020-05-07 | add set dAPA v dIC |
| html | a9de4a1 | brimittleman | 2020-05-04 | Build site. |
| Rmd | b140367 | brimittleman | 2020-05-04 | add pie charts |
| html | f8b25dd | brimittleman | 2020-05-01 | Build site. |
| Rmd | c78e612 | brimittleman | 2020-05-01 | add dic with others |
| html | 6fbd157 | brimittleman | 2020-04-30 | Build site. |
| Rmd | e226517 | brimittleman | 2020-04-30 | info by ind |
| html | fa67b41 | brimittleman | 2020-04-28 | Build site. |
| Rmd | e51455f | brimittleman | 2020-04-28 | add h3 and info with other vars |
| html | f54a9a2 | brimittleman | 2020-04-28 | Build site. |
| Rmd | 38b1619 | brimittleman | 2020-04-28 | add dapa and info |
| html | 448aa08 | brimittleman | 2020-04-24 | Build site. |
| Rmd | 93d00f3 | brimittleman | 2020-04-24 | add info content |
| html | 53a7570 | brimittleman | 2020-04-22 | Build site. |
| Rmd | b4e617e | brimittleman | 2020-04-22 | add color and prop dom, add decay |
| html | 9d14c53 | brimittleman | 2020-04-22 | Build site. |
| Rmd | 2207128 | brimittleman | 2020-04-22 | add prot to dom and add effect size plots |
| html | d01cd84 | brimittleman | 2020-04-21 | Build site. |
| Rmd | 0f53338 | brimittleman | 2020-04-21 | add de and diff dom mech |
| html | fbc6599 | brimittleman | 2020-04-21 | Build site. |
| Rmd | 95685ef | brimittleman | 2020-04-21 | add length diff analysis |
| html | a60094e | brimittleman | 2020-04-21 | Build site. |
| Rmd | 2b63d02 | brimittleman | 2020-04-21 | add new dom and de/dapa |
| html | 3e42f78 | brimittleman | 2020-04-20 | Build site. |
| Rmd | b00be28 | brimittleman | 2020-04-20 | add new dom to anaylses |
| html | 25d194e | brimittleman | 2020-04-20 | Build site. |
| Rmd | 40ba921 | brimittleman | 2020-04-20 | add effect size with dom |
| html | 1dc519a | brimittleman | 2020-04-17 | Build site. |
| Rmd | 9f8e75f | brimittleman | 2020-04-17 | add enrich |
| html | 8f48b3a | brimittleman | 2020-04-17 | Build site. |
| Rmd | 1d7b9d2 | brimittleman | 2020-04-17 | add diff top 2 sec |
| html | 218a3d4 | brimittleman | 2020-04-16 | Build site. |
| Rmd | 2461fb7 | brimittleman | 2020-04-16 | new dom integration |
| html | 38c6dc9 | brimittleman | 2020-04-14 | Build site. |
| Rmd | 2d0668e | brimittleman | 2020-04-14 | add new way to call dom |
| html | edd8940 | brimittleman | 2020-04-13 | Build site. |
| Rmd | 6997920 | brimittleman | 2020-04-13 | initial miRNA |
| html | 88b3edd | brimittleman | 2020-04-13 | Build site. |
| Rmd | c5fc23c | brimittleman | 2020-04-13 | add long short info |
| html | a7e29b9 | brimittleman | 2020-04-10 | Build site. |
| Rmd | 014951a | brimittleman | 2020-04-10 | remove 18499 |
| html | 83ab280 | brimittleman | 2020-04-09 | Build site. |
| Rmd | 21e8a4f | brimittleman | 2020-04-09 | remove ind map |
| html | 7968e3c | brimittleman | 2020-04-09 | Build site. |
| Rmd | fc93eb9 | brimittleman | 2020-04-09 | red for no 18499 |
| html | 60a370d | brimittleman | 2020-04-08 | Build site. |
| Rmd | 4fd3903 | brimittleman | 2020-04-08 | add corr betweenfrac |
| html | 4c131c9 | brimittleman | 2020-04-08 | Build site. |
| Rmd | 2f5d4d5 | brimittleman | 2020-04-08 | change number and add 3; utr |
| html | e45850e | brimittleman | 2020-04-08 | Build site. |
| Rmd | 856c506 | brimittleman | 2020-04-08 | fix labels |
| html | 5e58f03 | brimittleman | 2020-04-08 | Build site. |
| html | d81b148 | brimittleman | 2020-04-07 | Build site. |
| Rmd | a672b02 | brimittleman | 2020-04-07 | numb dist for dom |
| html | 7877726 | brimittleman | 2020-04-07 | Build site. |
| Rmd | 81e9838 | brimittleman | 2020-04-07 | add pol2 initial data |
| html | b3cce4d | brimittleman | 2020-04-06 | Build site. |
| Rmd | 71101c1 | brimittleman | 2020-04-06 | add dom pattern and de |
| html | a281849 | brimittleman | 2020-04-06 | Build site. |
| Rmd | 637094a | brimittleman | 2020-04-06 | look at total dominance |
| html | c2a0778 | brimittleman | 2020-04-06 | Build site. |
| Rmd | 9676d72 | brimittleman | 2020-04-06 | updated anno |
| html | 2242e4a | brimittleman | 2020-04-06 | Build site. |
| Rmd | 92f06e4 | brimittleman | 2020-04-06 | update anno |
| html | c59a7de | brimittleman | 2020-04-05 | Build site. |
| Rmd | 68c949f | brimittleman | 2020-04-05 | update post sno |
| html | 065ffdc | brimittleman | 2020-04-03 | Build site. |
| Rmd | 8269a9a | brimittleman | 2020-04-03 | update post sno |
| html | 72ab9ea | brimittleman | 2020-04-03 | Build site. |
| Rmd | 767bb78 | brimittleman | 2020-04-03 | update anno |
| html | 4722051 | brimittleman | 2020-04-02 | Build site. |
| Rmd | 9ba1428 | brimittleman | 2020-04-02 | add start of merge analysis |
| html | 3b7192e | brimittleman | 2020-04-02 | Build site. |
| Rmd | 788b72c | brimittleman | 2020-04-02 | add list of problems |
| html | 04171bc | brimittleman | 2020-04-02 | Build site. |
| Rmd | c761757 | brimittleman | 2020-04-02 | add normalized |
| html | 348d9fe | brimittleman | 2020-04-01 | Build site. |
| Rmd | 0679399 | brimittleman | 2020-04-01 | add no tie analysis |
| html | 8cb8b0a | brimittleman | 2020-04-01 | Build site. |
| Rmd | 7447f2d | brimittleman | 2020-04-01 | add norm dom and add filter comp plots |
| html | 1274a02 | brimittleman | 2020-03-30 | Build site. |
| Rmd | 2052494 | brimittleman | 2020-03-30 | add dom with primary |
| html | a70f2fe | brimittleman | 2020-03-28 | Build site. |
| Rmd | 706fa0d | brimittleman | 2020-03-28 | add mm exp code |
| html | 3d4dd47 | brimittleman | 2020-03-27 | Build site. |
| Rmd | f92b89c | brimittleman | 2020-03-26 | add ortho exon and new mm |
| html | 10fb0fb | brimittleman | 2020-03-25 | Build site. |
| Rmd | 6adb4d8 | brimittleman | 2020-03-25 | add check res no MM |
| html | f180064 | brimittleman | 2020-03-24 | Build site. |
| Rmd | 73127b5 | brimittleman | 2020-03-24 | add con and dom |
| html | eebb319 | brimittleman | 2020-03-23 | Build site. |
| Rmd | 81d06e8 | brimittleman | 2020-03-23 | add remove sno analysis |
| html | 246d60c | brimittleman | 2020-03-19 | Build site. |
| Rmd | b6ccdbc | brimittleman | 2020-03-19 | add new quat |
| html | 020ff7b | brimittleman | 2020-03-19 | Build site. |
| Rmd | 01f2aba | brimittleman | 2020-03-19 | add start to coding pas explore |
| html | 050da80 | brimittleman | 2020-03-18 | Build site. |
| Rmd | 536958c | brimittleman | 2020-03-18 | add res for overlapping PAS |
| html | 74e186a | brimittleman | 2020-03-17 | Build site. |
| Rmd | e85defb | brimittleman | 2020-03-17 | add res from diff mis prime filters |
| html | 63212bb | brimittleman | 2020-03-17 | Build site. |
| 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 |
| html | 30bfaaa | brimittleman | 2020-03-16 | Build site. |
| 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 |
| html | d1e9351 | brimittleman | 2020-03-13 | Build site. |
| Rmd | 0445720 | brimittleman | 2020-03-13 | add map stats when you remove Ns |
| html | 51190b4 | brimittleman | 2020-03-09 | Build site. |
| html | f1ec3e0 | brimittleman | 2020-03-09 | Build site. |
| Rmd | 552842c | brimittleman | 2020-03-09 | add TvN |
| html | 25a4790 | brimittleman | 2020-03-07 | Build site. |
| Rmd | c6a11f0 | brimittleman | 2020-03-07 | add expression indep |
| html | 22926ec | brimittleman | 2020-03-06 | Build site. |
| Rmd | 680d435 | brimittleman | 2020-03-06 | add ptm analysis |
| html | a1fd883 | brimittleman | 2020-03-05 | Build site. |
| Rmd | a71e15c | brimittleman | 2020-03-05 | wflow_publish(c(“analysis/index.Rmd”, “analysis/DirSelectionKhan.Rmd”)) |
| html | 7b73ce7 | brimittleman | 2020-03-04 | Build site. |
| Rmd | ad95271 | brimittleman | 2020-03-04 | add upstream control |
| html | 09ad482 | brimittleman | 2020-02-24 | Build site. |
| Rmd | 7385496 | brimittleman | 2020-02-24 | add correlations plotted by location |
| html | 5f821ee | brimittleman | 2020-02-23 | Build site. |
| Rmd | f4ae857 | brimittleman | 2020-02-23 | wflow_publish(c(“analysis/index.Rmd”, “analysis/DiffUsedIntronic.Rmd”)) |
| html | 5bcde2f | brimittleman | 2020-02-21 | Build site. |
| Rmd | 2e8ed44 | brimittleman | 2020-02-21 | add Splice site strength |
| html | f02217e | brimittleman | 2020-01-28 | Build site. |
| Rmd | 86aabf2 | brimittleman | 2020-01-28 | add expression overlap with APA exploration |
| html | b1b07d5 | brimittleman | 2020-01-25 | Build site. |
| html | 9642296 | brimittleman | 2020-01-23 | Build site. |
| Rmd | 1673f18 | brimittleman | 2020-01-23 | start the prot mediation cant do diff indiv |
| html | 838da9b | brimittleman | 2020-01-23 | Build site. |
| Rmd | a018c33 | brimittleman | 2020-01-23 | add diff usgage and ss |
| html | 2d84fb1 | brimittleman | 2020-01-23 | Build site. |
| 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 |
| html | f2421a4 | brimittleman | 2020-01-22 | Build site. |
| Rmd | d886866 | brimittleman | 2020-01-22 | add correlation between pheno DF |
| html | 8536528 | brimittleman | 2020-01-22 | Build site. |
| Rmd | 07fd459 | brimittleman | 2020-01-22 | DF for upset and translation protein ven |
| html | 5800231 | brimittleman | 2020-01-21 | Build site. |
| Rmd | 117fd63 | brimittleman | 2020-01-21 | redo differential analysis with double filt |
| html | f002978 | brimittleman | 2020-01-21 | Build site. |
| Rmd | 46c489b | brimittleman | 2020-01-21 | nuclear diff filtered |
| html | 6c39a2a | brimittleman | 2020-01-21 | Build site. |
| 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 | 2019-11-23 | 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.
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
Test relationship is driven by switching 3’ UTR pas and intronic
List of everything we tried for this section:
Liftover
Annotate and make phenotype
Evaluate results:
From before reseq:
From the original nuclear dominant