Last updated: 2019-01-01

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• ✔ R Markdown file: up-to-date

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• ✔ Repository version: 5c937b2

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  Ignored files:
      Ignored:    code/.ipynb_checkpoints/
      Ignored:    output/10x-180504
      Ignored:    output/10x-180504-aligned
      Ignored:    output/10x-180504-aligned-metageneplot
      Ignored:    output/10x-180504-beforeQC
      Ignored:    output/10x-180504-beforeqc
      Ignored:    output/10x-180504-cca-discardedcells
      Ignored:    output/10x-180504-ccregout
      Ignored:    output/10x-180504-ccregout-aligned
      Ignored:    output/10x-180504-ccregout-cca-discardedcells
      Ignored:    output/10x-180831
      Ignored:    output/10x-180831-T1T2T3
      Ignored:    output/10x-180831-T4T5
      Ignored:    output/10x-180831-beforeqc
      Ignored:    output/10x-180831-notcleaned
      Ignored:    output/monocle/
  
  Untracked files:
      Untracked:  code/mixture_cluster_gsea.R
      Untracked:  tables/10x-180504-stressed-cells-analysis.txt
      Untracked:  tables/GSEA_mixture-cluster.txt
      Untracked:  tables/Revigo_input_mixture-cluster.txt
      Untracked:  tables/Revigo_mixture-cluster.csv
      Untracked:  tables/Revigo_mixture-cluster_cleaned.txt
  
  Unstaged changes:
      Modified:   analysis/10x-180504-general-analysis.Rmd
      Modified:   analysis/10x-180831-general-analysis.Rmd
      Modified:   plots/180504_mixture.pdf
  
  

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File	Version	Author	Date	Message
Rmd	5c937b2	PytrikFolkertsma	2019-01-01	wflow_publish(c(“analysis/index.Rmd”))
Rmd	1ee9efb	PytrikFolkertsma	2019-01-01	updated notebooks
html	12351bf	PytrikFolkertsma	2019-01-01	Build site.
Rmd	b88a9ba	PytrikFolkertsma	2019-01-01	wflow_publish(c(“analysis/10x-180504-monocle.Rmd”, “analysis/index.Rmd”))
Rmd	3be3c3d	PytrikFolkertsma	2018-12-12	updates
html	092644e	PytrikFolkertsma	2018-11-11	Build site.
Rmd	f649370	PytrikFolkertsma	2018-11-11	wflow_publish(c(“analysis/index.Rmd”))
html	0652285	PytrikFolkertsma	2018-11-08	Build site.
Rmd	0870772	PytrikFolkertsma	2018-11-08	wflow_publish(c(“analysis/index.Rmd”))
html	19d224c	PytrikFolkertsma	2018-11-08	Build site.
Rmd	a40cd08	PytrikFolkertsma	2018-11-08	wflow_publish(c(“analysis/index.Rmd”))
html	072f174	PytrikFolkertsma	2018-11-08	Build site.
html	6e36947	PytrikFolkertsma	2018-11-07	Build site.
html	8c816d4	PytrikFolkertsma	2018-11-07	Build site.
html	4b12f43	PytrikFolkertsma	2018-11-05	Build site.
Rmd	f6e9077	PytrikFolkertsma	2018-11-05	wflow_publish(c(“analysis/10x-180504-beforeQC.Rmd”, “analysis/index.Rmd”))
html	9e51a0a	PytrikFolkertsma	2018-11-02	Build site.
html	cc9ed00	PytrikFolkertsma	2018-11-02	Build site.
Rmd	d7744be	PytrikFolkertsma	2018-11-02	wflow_publish(c(“analysis/index.Rmd”))
html	0eee1c4	PytrikFolkertsma	2018-11-02	Build site.
Rmd	bbcb1c5	PytrikFolkertsma	2018-11-02	wflow_publish(c(“analysis/index.Rmd”))
html	4f5e908	PytrikFolkertsma	2018-11-02	Build site.
Rmd	b2747c4	PytrikFolkertsma	2018-11-02	wflow_publish(c(“analysis/index.Rmd”))
html	2b95cbd	PytrikFolkertsma	2018-11-02	Build site.
Rmd	a70776e	PytrikFolkertsma	2018-11-02	wflow_publish(c(“analysis/index.Rmd”))
html	d6ccbf9	PytrikFolkertsma	2018-11-02	Build site.
Rmd	5ef5a54	PytrikFolkertsma	2018-11-02	wflow_publish(c(“analysis/index.Rmd”))
html	77f0cd0	PytrikFolkertsma	2018-11-02	Build site.
Rmd	ad3b515	PytrikFolkertsma	2018-11-02	wflow_publish(c(“analysis/index.Rmd”))
html	b20b10d	PytrikFolkertsma	2018-11-02	Build site.
Rmd	7f1e2a3	PytrikFolkertsma	2018-11-02	wflow_publish(c(“analysis/index.Rmd”))
html	a58d589	PytrikFolkertsma	2018-11-02	Build site.
Rmd	9faddbb	PytrikFolkertsma	2018-11-02	wflow_publish(c(“analysis/index.Rmd”))
html	f378262	PytrikFolkertsma	2018-11-02	Build site.
html	4d75489	PytrikFolkertsma	2018-11-02	Build site.
Rmd	032862e	PytrikFolkertsma	2018-11-02	wflow_publish(c(“analysis/index.Rmd”))
html	ca069c3	PytrikFolkertsma	2018-11-02	notebooks + index
html	cb4228f	PytrikFolkertsma	2018-11-02	Build site.
Rmd	e39c768	PytrikFolkertsma	2018-11-02	wflow_publish(c(“analysis/index.Rmd”))
html	a4453ec	PytrikFolkertsma	2018-11-02	Build site.
Rmd	52e9177	PytrikFolkertsma	2018-11-02	wflow_publish(c(“analysis/index.Rmd”))
html	b5866be	PytrikFolkertsma	2018-11-02	Build site.
Rmd	42be16c	PytrikFolkertsma	2018-11-02	wflow_publish(c(“analysis/index.Rmd”))
html	17b0321	PytrikFolkertsma	2018-11-02	Build site.
Rmd	20adbe0	PytrikFolkertsma	2018-11-02	wflow_publish(c(“analysis/index.Rmd”))
html	91f2c9c	PytrikFolkertsma	2018-11-02	Build site.
Rmd	f8fe591	PytrikFolkertsma	2018-11-02	wflow_publish(c(“analysis/index.Rmd”))
html	eaa7e4a	PytrikFolkertsma	2018-11-02	Build site.
Rmd	120215c	PytrikFolkertsma	2018-11-02	general analysis + alignment
html	d810265	PytrikFolkertsma	2018-10-31	Build site.
html	57c44d6	PytrikFolkertsma	2018-10-31	Build site.
html	1f7e0da	PytrikFolkertsma	2018-10-30	Build site.
html	3395a74	PytrikFolkertsma	2018-10-26	first commit
Rmd	cf98ea8	PytrikFolkertsma	2018-10-26	Start workflowr project.

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Notebooks for 10x-180504 analysis:

1. Before QC
2. General analysis
3. Alignment
4. Differentially expressed genes between depots
5. Monocle analysis
6. Velocyto analysis
7. Scmap analysis
8. Mixture cluster
9. Marker genes

Notebooks for 10x-180831 analysis:

1. First data inspection
2. General analysis
3. Monocle analysis
4. Velocyto analysis

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This reproducible R Markdown analysis was created with workflowr 1.1.1

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