Last updated: 2020-02-11
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Knit directory: apaQTL/analysis/
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Unstaged changes:
Modified: analysis/ExploreNpas.Rmd
Modified: analysis/NuclearSpecIncludeNotTested.Rmd
Modified: analysis/PASdescriptiveplots.Rmd
Modified: analysis/Readdistagainstfeatures.Rmd
Modified: analysis/TSS.Rmd
Modified: analysis/decayAndStability.Rmd
Modified: analysis/miRNAdisrupt.Rmd
Modified: analysis/nascenttranscription.Rmd
Modified: analysis/nucSpecinEQTLs.Rmd
Modified: analysis/overlapapaqtlsandeqtls.Rmd
Modified: analysis/pQTLexampleplot.Rmd
Modified: analysis/propeQTLs_explained.Rmd
Modified: analysis/version15bpfilter.Rmd
Modified: code/DistPAS2Sig.py
Modified: code/Script4NuclearQTLexamples.sh
Modified: code/Script4TotalQTLexamples.sh
Modified: code/apaQTLsnake.err
Modified: code/run_qtlFacetBoxplots.sh
Deleted: code/test.txt
Deleted: reads_graphs.Rmd
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| Rmd | 66100b8 | brimittleman | 2020-02-11 | add tot v nuc effect size info and mech |
| html | 38ece5e | brimittleman | 2020-02-09 | Build site. |
| Rmd | 0ea6bf8 | brimittleman | 2020-02-09 | add mirna disrupt analysis |
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| Rmd | 76c8064 | brimittleman | 2020-02-06 | add effect size plot for eQTL |
| html | ad502c6 | brimittleman | 2020-02-04 | Build site. |
| Rmd | ee3c3a8 | brimittleman | 2020-02-04 | add base comp analysis around PAS |
| html | 723946b | brimittleman | 2020-02-02 | Build site. |
| Rmd | d0f4f33 | brimittleman | 2020-02-02 | add TSS analysis |
| html | ddfe841 | brimittleman | 2020-01-31 | Build site. |
| Rmd | a1607df | brimittleman | 2020-01-31 | look at tissue specifcity |
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| Rmd | 3a8156f | brimittleman | 2020-01-31 | wflow_publish(c(“analysis/index.Rmd”, “analysis/ConservationPAS.Rmd”)) |
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| Rmd | 97fee76 | brimittleman | 2020-01-31 | add var ribo and apap |
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| Rmd | fd5ccd7 | brimittleman | 2020-01-30 | add LD regress notes and first var in apa |
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| Rmd | 97dec83 | brimittleman | 2020-01-30 | add decay and stability, nmd analysis |
| html | 8a3d1ea | brimittleman | 2019-11-08 | Build site. |
| Rmd | d72c604 | brimittleman | 2019-11-08 | add first intron analysis |
| html | 5b3df80 | brimittleman | 2019-09-26 | Build site. |
| Rmd | aa30fa2 | brimittleman | 2019-09-26 | add new dt plots analysis |
| html | 3af0253 | brimittleman | 2019-09-17 | Build site. |
| Rmd | f8cb7b8 | brimittleman | 2019-09-17 | move inclusive, get numbers for paper |
| html | 2bc4187 | brimittleman | 2019-09-15 | Build site. |
| Rmd | 7c4debc | brimittleman | 2019-09-15 | add inclusive PAS analysis |
| html | bb2fbab | brimittleman | 2019-09-11 | Build site. |
| Rmd | 5ad175a | brimittleman | 2019-09-11 | udate pas graphs and asdd total |
| html | 42f352c | brimittleman | 2019-09-07 | Build site. |
| Rmd | c5c6546 | brimittleman | 2019-09-07 | add enrichment analysis |
| html | 3b25860 | brimittleman | 2019-09-04 | Build site. |
| Rmd | 5984fad | brimittleman | 2019-09-04 | update for new filter condition |
| html | 07d9709 | brimittleman | 2019-08-28 | Build site. |
| Rmd | d5f19cc | brimittleman | 2019-08-28 | add new QC files to index |
| html | 4cd5f28 | brimittleman | 2019-08-26 | Build site. |
| Rmd | 5289aa1 | brimittleman | 2019-08-26 | add extra MP qc |
| html | 191d71f | brimittleman | 2019-08-07 | Build site. |
| Rmd | 01d0be5 | brimittleman | 2019-08-07 | add reads_graph analysis |
| html | d13025b | brimittleman | 2019-07-31 | Build site. |
| Rmd | e2ff61a | brimittleman | 2019-07-31 | add mayher plot to site |
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| Rmd | f3e3e16 | brimittleman | 2019-07-25 | small edits from paper writing and add gwas analysis |
| html | fb1fde6 | brimittleman | 2019-07-16 | Build site. |
| Rmd | 2572d13 | brimittleman | 2019-07-16 | add compare annotated and additional coverage |
| html | 272b0b4 | brimittleman | 2019-07-08 | Build site. |
| Rmd | b1e6dd1 | brimittleman | 2019-07-08 | update ptt analysis |
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| Rmd | f85f6d0 | brimittleman | 2019-07-07 | add ptt eqtls |
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| Rmd | bd5f228 | brimittleman | 2019-07-07 | add nuc spec eqtl res |
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| Rmd | 75b84f4 | brimittleman | 2019-07-01 | add code premature term |
| html | 5edd9c7 | brimittleman | 2019-06-30 | Build site. |
| Rmd | 709b4c8 | brimittleman | 2019-06-30 | add two reg |
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| Rmd | f00669b | brimittleman | 2019-06-28 | add GO |
| html | 1e58d07 | brimittleman | 2019-06-27 | Build site. |
| Rmd | db5d2e6 | brimittleman | 2019-06-27 | add pqtl example |
| html | 5d97550 | brimittleman | 2019-06-25 | Build site. |
| Rmd | 3e288f8 | brimittleman | 2019-06-25 | add tf analysis |
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| Rmd | 78dd5da | brimittleman | 2019-06-24 | add snp in ss analysis |
| html | fcab450 | brimittleman | 2019-06-21 | Build site. |
| Rmd | 5c83496 | brimittleman | 2019-06-21 | fix html typo |
| html | cd60f50 | brimittleman | 2019-06-20 | Build site. |
| Rmd | 6df08b6 | brimittleman | 2019-06-20 | change analysis to include not tested in total as nuc spec |
| html | 529a38a | brimittleman | 2019-06-18 | Build site. |
| Rmd | 63e21ea | brimittleman | 2019-06-18 | add credible set analysis |
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| Rmd | 01bc8aa | brimittleman | 2019-06-18 | add verify first inton res |
| html | 743c9c6 | brimittleman | 2019-06-17 | Build site. |
| Rmd | bc3ddae | brimittleman | 2019-06-17 | add effect size nuc spec |
| html | 2b8bf0c | brimittleman | 2019-06-17 | Build site. |
| Rmd | 54946d7 | brimittleman | 2019-06-17 | add mol qtl code |
| html | 44d1fcc | brimittleman | 2019-06-16 | Build site. |
| Rmd | a5430c3 | brimittleman | 2019-06-16 | add qtl and usage analysis |
| html | 3fbf3f3 | brimittleman | 2019-06-14 | Build site. |
| Rmd | dc8d012 | brimittleman | 2019-06-14 | add nuclear specific analysis |
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| Rmd | b38964e | brimittleman | 2019-06-14 | add pqtl overlap |
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| Rmd | bf91cb3 | brimittleman | 2019-06-14 | add location plot |
| html | 2c39fd1 | brimittleman | 2019-06-11 | Build site. |
| html | 9820e7e | brimittleman | 2019-06-11 | Build site. |
| Rmd | abd1ae9 | brimittleman | 2019-06-11 | add geno proc info |
| html | 5d71c2e | brimittleman | 2019-06-10 | Build site. |
| Rmd | c5fe1c2 | brimittleman | 2019-06-10 | add motif disruption |
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| Rmd | 02d97db | brimittleman | 2019-06-07 | add intron ratio file |
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| Rmd | 32091ee | brimittleman | 2019-06-07 | more prop explained to new analysis |
| html | 4c50025 | brimittleman | 2019-06-06 | Build site. |
| Rmd | 8710e5c | brimittleman | 2019-06-06 | add new analysis for unex v ex |
| html | 0e20f3a | brimittleman | 2019-06-05 | Build site. |
| Rmd | c743502 | brimittleman | 2019-06-05 | first pass overlap |
| html | d30d453 | brimittleman | 2019-05-30 | Build site. |
| Rmd | 1321989 | brimittleman | 2019-05-30 | add chromhmm analysis |
| html | a71262e | brimittleman | 2019-05-29 | Build site. |
| Rmd | 6432c1b | brimittleman | 2019-05-29 | inititate nascent analysis |
| html | 28c8ca3 | brimittleman | 2019-05-24 | Build site. |
| Rmd | 3f63045 | brimittleman | 2019-05-24 | add code to prepare non norm qtl |
| html | a88eedf | brimittleman | 2019-05-20 | Build site. |
| Rmd | 8f883d8 | brimittleman | 2019-05-20 | add overlap analysis |
| html | d89772d | brimittleman | 2019-05-15 | Build site. |
| Rmd | ee92964 | brimittleman | 2019-05-15 | start ideas for inton analysis |
| html | 81a3e16 | brimittleman | 2019-05-15 | Build site. |
| Rmd | f484dcd | brimittleman | 2019-05-15 | add nascent transcription plot |
| html | 35b1f6e | brimittleman | 2019-05-15 | Build site. |
| Rmd | 90e0c4d | brimittleman | 2019-05-15 | add reg heatmap |
| html | bf3a1e0 | brimittleman | 2019-05-14 | Build site. |
| Rmd | 77ca26a | brimittleman | 2019-05-14 | results by logef |
| html | 144c00b | brimittleman | 2019-05-08 | Build site. |
| Rmd | 5e39f1c | brimittleman | 2019-05-08 | choose pcs and start qtl rerun |
| html | f5af9c6 | brimittleman | 2019-05-08 | Build site. |
| Rmd | 1ba7d2b | brimittleman | 2019-05-08 | add pca |
| html | 9062ebd | brimittleman | 2019-05-03 | Build site. |
| Rmd | 0e5af55 | brimittleman | 2019-05-03 | add utr coverage |
| html | 53eeea4 | brimittleman | 2019-05-02 | Build site. |
| Rmd | 2067946 | brimittleman | 2019-05-02 | add old vs new data usage analysis |
| html | 60093ce | brimittleman | 2019-05-02 | Build site. |
| Rmd | 24c2ceb | brimittleman | 2019-05-02 | add diff iso |
| html | ac656aa | brimittleman | 2019-04-30 | Build site. |
| Rmd | f9b8195 | brimittleman | 2019-04-30 | understand usage of new pas |
| html | e3bdc3a | brimittleman | 2019-04-29 | Build site. |
| Rmd | 39a6572 | brimittleman | 2019-04-29 | add correlation genotype heatmap |
| html | be227e7 | brimittleman | 2019-04-25 | Build site. |
| Rmd | 6cb0a99 | brimittleman | 2019-04-25 | add seq meta pltos |
| html | b2525c3 | brimittleman | 2019-04-24 | Build site. |
| Rmd | 9bbe437 | brimittleman | 2019-04-24 | add corr analysis |
| html | 214c05c | brimittleman | 2019-04-23 | Build site. |
| Rmd | 27b11e3 | brimittleman | 2019-04-23 | start signal site analysis |
| Rmd | 02e580f | brimittleman | 2019-04-23 | add desc plots |
| html | 1fb7086 | brimittleman | 2019-04-23 | Build site. |
| Rmd | 544b1d9 | brimittleman | 2019-04-23 | add pas descriptive plots |
| html | e650e08 | brimittleman | 2019-04-22 | Build site. |
| Rmd | 851c963 | brimittleman | 2019-04-22 | add reads against feature |
| html | 28bd046 | brimittleman | 2019-04-18 | Build site. |
| Rmd | 017f5c0 | brimittleman | 2019-04-18 | add map apa qtl pipeline |
| html | 874081d | brimittleman | 2019-04-18 | Build site. |
| Rmd | 22bfb66 | brimittleman | 2019-04-18 | add pas usage qc analysis |
| html | aab1fca | brimittleman | 2019-04-17 | Build site. |
| Rmd | 057dc1a | brimittleman | 2019-04-17 | add bam 2 pas analysis |
| Rmd | 13484a9 | brimittleman | 2019-04-13 | re-add analysis |
| html | fd1f8cb | brimittleman | 2019-04-13 | Build site. |
| Rmd | 549c7ff | brimittleman | 2019-04-12 | add helper scripts for pas snake |
| html | 549c7ff | brimittleman | 2019-04-12 | add helper scripts for pas snake |
| Rmd | f5e23f3 | brimittleman | 2019-04-11 | add fastq 2 bam |
| html | 444f1c7 | brimittleman | 2019-04-11 | Build site. |
| html | 1c955c5 | brimittleman | 2019-04-11 | Build site. |
| Rmd | 0f343f8 | brimittleman | 2019-04-11 | Start workflowr project. |
Welcome to my research website.
In the preprocessing steps of the analysis I will go from the fastq files that come off the sequencer to the PAS I will use for the rest of the analysis.
These files create some of the QC metrics I used for the analysis.
Revisions (Thank you to the reviewers for suggestions)