Last updated: 2019-06-14
Checks: 2 0
Knit directory: apaQTL/analysis/
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Unstaged changes:
Modified: analysis/Readdistagainstfeatures.Rmd
Modified: analysis/intonRNAratio.Rmd
Modified: analysis/nascentRNA.Rmd
Modified: analysis/overlapapaqtlsandeqtls.Rmd
Modified: code/BothFracDTPlotGeneRegions.sh
Modified: code/Snakefile
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Modified: code/apaQTLCorrectPvalMakeQQ.R
Modified: code/apaQTL_Nominal.sh
Modified: code/apaQTL_permuted.sh
Modified: code/apaQTLsnake.err
Modified: code/bam2bw.sh
Modified: code/bed2saf.py
Modified: code/cluster.json
Modified: code/clusterfiltPAS.json
Modified: code/config.yaml
Modified: code/environment.yaml
Modified: code/makePheno.py
Deleted: code/test.txt
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | b38964e | brimittleman | 2019-06-14 | add pqtl overlap |
| html | 4912eaa | brimittleman | 2019-06-14 | Build site. |
| 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 |
| html | f81a440 | brimittleman | 2019-06-07 | Build site. |
| Rmd | 02d97db | brimittleman | 2019-06-07 | add intron ratio file |
| html | 458e494 | brimittleman | 2019-06-07 | Build site. |
| 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. |
| 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. |
| 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. |
| html | be227e7 | brimittleman | 2019-04-25 | Build site. |
| 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 |
| html | 1fb7086 | brimittleman | 2019-04-23 | Build site. |
| 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 |
| html | fd1f8cb | brimittleman | 2019-04-13 | Build site. |
| 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.