Last updated: 2018-10-08
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Unstaged changes:
Modified: analysis/28ind.peak.explore.Rmd
Modified: analysis/39indQC.Rmd
Modified: analysis/PeakToGeneAssignment.Rmd
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File | Version | Author | Date | Message |
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html | 7369f8e | Briana Mittleman | 2018-10-02 | Build site. |
Rmd | f66679b | Briana Mittleman | 2018-10-02 | overlap plots at peak level |
html | 2e0d959 | Briana Mittleman | 2018-10-01 | Build site. |
Rmd | 9d6ee03 | Briana Mittleman | 2018-10-01 | add 4su plots |
html | da0f70e | Briana Mittleman | 2018-10-01 | Build site. |
Rmd | fecb046 | Briana Mittleman | 2018-10-01 | fix overlapfile |
html | ac983db | Briana Mittleman | 2018-10-01 | Build site. |
Rmd | 35142fb | Briana Mittleman | 2018-10-01 | overlap QTL plots |
html | 149d033 | Briana Mittleman | 2018-09-26 | Build site. |
html | aaed5fd | Briana Mittleman | 2018-09-26 | Build site. |
Rmd | eda266e | Briana Mittleman | 2018-09-26 | test peak to gene transcript dist |
html | 47cd4bf | Briana Mittleman | 2018-09-26 | Build site. |
html | b1bcf99 | Briana Mittleman | 2018-09-25 | Build site. |
html | d3bb287 | Briana Mittleman | 2018-09-24 | Build site. |
Rmd | f7934ce | Briana Mittleman | 2018-09-24 | wflow_publish(c(“index.Rmd”, “39indQC.Rmd”)) |
html | f92a58f | Briana Mittleman | 2018-09-06 | Build site. |
Rmd | 46b7343 | Briana Mittleman | 2018-09-06 | add overlap analysis with code to subset |
html | b4bda1b | Briana Mittleman | 2018-08-30 | Build site. |
html | e000583 | Briana Mittleman | 2018-08-30 | Build site. |
Rmd | a5f5276 | Briana Mittleman | 2018-08-30 | initialize diff iso pipeline |
html | c6dc97b | brimittleman | 2018-08-28 | Build site. |
html | 5564e25 | brimittleman | 2018-08-20 | Build site. |
Rmd | 6b1b51c | brimittleman | 2018-08-20 | start qtl analsis, add to index |
html | c67380e | brimittleman | 2018-08-14 | Build site. |
html | 38bfbaf | brimittleman | 2018-08-09 | Build site. |
Rmd | 03761cb | brimittleman | 2018-08-09 | start peak explore analysis for 54 libraries |
html | e5a8da6 | Briana Mittleman | 2018-07-30 | Build site. |
Rmd | 422a428 | Briana Mittleman | 2018-07-30 | add peak cove pipeline and combined lane qc |
html | 0398fdb | Briana Mittleman | 2018-07-25 | Build site. |
Rmd | 2d41f11 | Briana Mittleman | 2018-07-25 | add expand smash to index |
html | 3a5a8fe | Briana Mittleman | 2018-07-25 | Build site. |
html | a34f9c1 | Briana Mittleman | 2018-07-17 | Build site. |
Rmd | ca9cee9 | Briana Mittleman | 2018-07-17 | add smash test to index |
html | c3ca148 | Briana Mittleman | 2018-07-17 | Build site. |
html | dc4a51a | Briana Mittleman | 2018-07-16 | Build site. |
Rmd | 4fede84 | Briana Mittleman | 2018-07-16 | add eval brain analysis |
html | cfc8f43 | Briana Mittleman | 2018-07-13 | Build site. |
Rmd | 4a84769 | Briana Mittleman | 2018-07-13 | add analysis for coparing coverage of RNAseq and 3’ seq |
html | 210cd2b | Briana Mittleman | 2018-07-05 | Build site. |
Rmd | 8b622c3 | Briana Mittleman | 2018-07-05 | add denovo to index |
html | ee777df | Briana Mittleman | 2018-06-26 | Build site. |
Rmd | 789d8ef | Briana Mittleman | 2018-06-26 | start test macs analysis. download package |
html | 30b415e | Briana Mittleman | 2018-06-19 | Build site. |
html | 08b5934 | Briana Mittleman | 2018-06-13 | Build site. |
Rmd | 642faf0 | Briana Mittleman | 2018-06-13 | start PAS enrichment analysis |
html | 4ef7d85 | Briana Mittleman | 2018-06-11 | Build site. |
Rmd | 03c7b14 | Briana Mittleman | 2018-06-11 | start A analysis |
html | 062808d | Briana Mittleman | 2018-06-07 | Build site. |
html | 86cfd9f | Briana Mittleman | 2018-06-06 | Build site. |
Rmd | a19683c | Briana Mittleman | 2018-06-06 | start dif isoform analysis |
html | 710cf6a | Briana Mittleman | 2018-05-29 | Build site. |
Rmd | d58bc13 | Briana Mittleman | 2018-05-29 | start 200 bp analysis |
html | 96ecbb1 | Briana Mittleman | 2018-05-26 | Build site. |
Rmd | 2076ce9 | Briana Mittleman | 2018-05-26 | initial commit, gene level analysis |
html | b5cdd59 | Briana Mittleman | 2018-05-26 | Build site. |
Rmd | 9a49459 | Briana Mittleman | 2018-05-26 | start map qc analysis |
html | 924952b | Briana Mittleman | 2018-05-09 | Build site. |
Rmd | f8ce0fc | Briana Mittleman | 2018-05-09 | Update to 1.0 |
html | f8ce0fc | Briana Mittleman | 2018-05-09 | Update to 1.0 |
html | 3dd80ef | Briana Mittleman | 2018-05-08 | Build site. |
Rmd | 519447d | Briana Mittleman | 2018-05-08 | Add total.nuc.rnaseq analysis |
html | 889c9c6 | Briana Mittleman | 2018-05-02 | Build site. |
html | 9d196cf | Briana Mittleman | 2018-05-02 | Build site. |
html | 972ef3e | Briana Mittleman | 2018-05-02 | Build site. |
Rmd | 6cc5321 | Briana Mittleman | 2018-05-02 | add home page information |
html | e12dd6c | Briana Mittleman | 2018-05-01 | Build site. |
Rmd | 0e95115 | Briana Mittleman | 2018-05-01 | add home page information |
html | 4c26d4c | Briana Mittleman | 2018-05-01 | Build site. |
Rmd | 539892a | Briana Mittleman | 2018-05-01 | Start workflowr project. |
Briana Mittleman
This is the site I will use for my human 3’ seq project. I will have my workflow and analysis here. The three prime seq protocol I am using is Lexogen, QuantSeq 3’ mRNA-Seq library kit. The first analysis will be on the total and nucleic fractions of the LCL used in the net-seq analysis found at https://brimittleman.github.io/Net-seq/
Initial analysis on RNA seq of nuclear and total fractions:
Initial analysis on first 32 3’ seq libraries:
Explore and filter mis-primming:
Peak calling:
Peak coverage/Nominal QTLs/Diff iso:
Rerun analysis opp strand:
Evaluate and learn from QTLs:
Analysis for all 39 indivduals:
Molecular QTL analysis and Overlap:
This reproducible R Markdown analysis was created with workflowr 1.1.1