Last updated: 2018-07-25
workflowr checks: (Click a bullet for more information) ✔ R Markdown file: up-to-date
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
✔ Repository version: 2d41f11
wflow_publish
or wflow_git_commit
). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .DS_Store
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: output/.DS_Store
Untracked files:
Untracked: data/18486.genecov.txt
Untracked: data/APApeaksYL.total.inbrain.bed
Untracked: data/YL-SP-18486-T_S9_R1_001-genecov.txt
Untracked: data/bedgraph_peaks/
Untracked: data/bin200.5.T.nuccov.bed
Untracked: data/bin200.Anuccov.bed
Untracked: data/bin200.nuccov.bed
Untracked: data/gene_cov/
Untracked: data/leafcutter/
Untracked: data/nuc6up/
Untracked: data/reads_mapped_three_prime_seq.csv
Untracked: data/smash.cov.results.bed
Untracked: data/smash.cov.results.csv
Untracked: data/smash.cov.results.txt
Untracked: data/smash_testregion/
Untracked: data/ssFC200.cov.bed
Untracked: output/picard/
Untracked: output/plots/
Untracked: output/qual.fig2.pdf
Unstaged changes:
Modified: analysis/dif.iso.usage.leafcutter.Rmd
Modified: analysis/explore.filters.Rmd
Modified: analysis/test.max2.Rmd
Modified: code/Snakefile
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.
File | Version | Author | Date | Message |
---|---|---|---|---|
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:
This reproducible R Markdown analysis was created with workflowr 1.1.1