Last updated: 2020-03-30
Checks: 2 0
Knit directory: Comparative_APA/analysis/
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Unstaged changes:
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| Rmd | d886866 | brimittleman | 2020-01-22 | add correlation between pheno DF |
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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 | 96b46ba | brimittleman | 2020-01-19 | add enrichment in apapQTLs |
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| Rmd | 7a9f608 | brimittleman | 2020-01-18 | finished benchmark |
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| Rmd | e1c6d25 | brimittleman | 2020-01-14 | add analysis on species spec PAS |
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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 |
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| 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 | 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 | 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 | d56d98c | brimittleman | 2019-12-05 | add opp map |
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| 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.
From here on, I did everything double filtered:
From here on, I did everything double filtered:
Liftover
Annotate and make phenotype
Evaluate results:
From before reseq:
From the original nuclear dominant