cellranger_count issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues2020-11-03T12:29:40-06:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/48Update multiqc version/references report2020-11-03T12:29:40-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate multiqc version/references report* Add pipeline zenodo references report
* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)* Add pipeline zenodo references report
* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)3.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/46Add simple integration CI test2020-11-03T12:29:40-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd simple integration CI testto branches except master and develop to test nextflow run on branchesto branches except master and develop to test nextflow run on branches3.0.0Gervaise 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 configshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/10Add ability to count additional features2020-06-21T13:57:51-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd ability to count additional featureshttps://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis
Ab
CRISPR
customhttps://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis
Ab
CRISPR
customPendingGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.edu