cellranger_count issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues2020-08-02T09:57:17-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/49Add test for astrocyte 0.3.12020-08-02T09:57:17-05:00Venkat MalladiAdd test for astrocyte 0.3.1# Summary
* [ ] Add test for astrocyte-specific test besides cli
* [ ] Add Badge for astrocyte
* [ ] Test for astrocyte 0.3.1 instead of loading astrocyte
/cc @ghenry# Summary
* [ ] Add test for astrocyte-specific test besides cli
* [ ] Add Badge for astrocyte
* [ ] Test for astrocyte 0.3.1 instead of loading astrocyte
/cc @ghenryGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/35Shiny App2020-08-02T09:57:09-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduShiny App# Shiny app which recreates count's web_summary.html
## Priority 1
* [x] Select dimentionality reduction type
1. PCA
2. tSNE
3. UMAP
* [x] Select clustering type
1. Graph-Based
2. KMeans 2-10
* [x] Plot
* [x] Show DEGs...# Shiny app which recreates count's web_summary.html
## Priority 1
* [x] Select dimentionality reduction type
1. PCA
2. tSNE
3. UMAP
* [x] Select clustering type
1. Graph-Based
2. KMeans 2-10
* [x] Plot
* [x] Show DEGs based on clustering type
## Priority 2
* [ ] Recreate QC page (or find a way to display multi-qc output)
* [ ] Re-calculate Cliff-Knee plot
* Rank order raw_feature_bc_matrix
* Color barcodes from filtered_feature_bc_matrix green... rest redJeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/34Create output plots2020-08-02T09:57:07-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduCreate output plots## output to:
>output/analysis/*/
## plot:
* PCA with graphclust labels
* tSNE with graphclust labels
* UMAP with graphclust labels
## data for plots in:
>output/count*/*/outs/analysis/
#### remember not to try and read the output dir...## output to:
>output/analysis/*/
## plot:
* PCA with graphclust labels
* tSNE with graphclust labels
* UMAP with graphclust labels
## data for plots in:
>output/count*/*/outs/analysis/
#### remember not to try and read the output dir for the input of the new process... instead in the counts processes add the files necessary to a new outputhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/16Move params out of main.nf2020-04-13T11:37:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMove params out of main.nfWait for astroycte update to handle custom configsWait for astroycte update to handle custom configs