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.RData
.RData
 
 
.Rhistory
.Rhistory
 
 
2h5ad2h5seurat_general_final.R
2h5ad2h5seurat_general_final.R
 
 
Copy_of_Vizgen_Showcase_Mouse_Liver_0_2_1.ipynb
Copy_of_Vizgen_Showcase_Mouse_Liver_0_2_1.ipynb
 
 
DARanalysisseuratrds.R
DARanalysisseuratrds.R
 
 
DRGBL71113ANALYSIS.R
DRGBL71113ANALYSIS.R
 
 
NETWORKTUTORIAL.pdf
NETWORKTUTORIAL.pdf
 
 
Plots_cristalografia (1).R
Plots_cristalografia (1).R
 
 
README.md
README.md
 
 
R_functions_scATAC.R
R_functions_scATAC.R
 
 
Vizgen_Showcase_Mouse_Brain.ipynb
Vizgen_Showcase_Mouse_Brain.ipynb
 
 
check_DEG_Retina_Zhen.R
check_DEG_Retina_Zhen.R
 
 
check_marksersHAS6tissue.R
check_marksersHAS6tissue.R
 
 
check_marksersHAS6tissue_v2.R
check_marksersHAS6tissue_v2.R
 
 
config.yaml
config.yaml
 
 
converth5ad2seurat.R
converth5ad2seurat.R
 
 
coverageplotmice.R
coverageplotmice.R
 
 
deganalysisDRGpricelabvisium.R
deganalysisDRGpricelabvisium.R
 
 
degsacrossconditions.R
degsacrossconditions.R
 
 
deployshinycellapp.R
deployshinycellapp.R
 
 
getbulkcountsseurat.R
getbulkcountsseurat.R
 
 
ggplotsfun.R
ggplotsfun.R
 
 
heatmap.R
heatmap.R
 
 
integrateobjseurat.R
integrateobjseurat.R
 
 
integrationseurat.R
integrationseurat.R
 
 
knsdegs.R
knsdegs.R
 
 
matchcollumsdataframes.R
matchcollumsdataframes.R
 
 
mergecsvfiles.R
mergecsvfiles.R
 
 
metainfo.R
metainfo.R
 
 
obj_marker_HAS_list_6T.rds
obj_marker_HAS_list_6T.rds
 
 
objallgenes.R
objallgenes.R
 
 
objmerfishpanelgenes.R
objmerfishpanelgenes.R
 
 
optic nerve_reclustering-Copy1.ipynb
optic nerve_reclustering-Copy1.ipynb
 
 
opticnerveanalysiswithscanpy.ipynb
opticnerveanalysiswithscanpy.ipynb
 
 
pathfindr.R
pathfindr.R
 
 
run_QCscATACsignacmice_multi.R
run_QCscATACsignacmice_multi.R
 
 
run_assignCelltype.R
run_assignCelltype.R
 
 
run_scrnaDEGs_Jehan.R
run_scrnaDEGs_Jehan.R
 
 
run_scrnadegs.R
run_scrnadegs.R
 
 
run_velocity_dynamical.py
run_velocity_dynamical.py
 
 
runcellranger.sh
runcellranger.sh
 
 
sample.txt
sample.txt
 
 
saverds.R
saverds.R
 
 
scATACfiguresplotsyang2022Paper.R
scATACfiguresplotsyang2022Paper.R
 
 
scRNAfiguresplotsyang2022Paper.R
scRNAfiguresplotsyang2022Paper.R
 
 
scanpy.ipynb
scanpy.ipynb
 
 
scpred.R
scpred.R
 
 
scrnadegs.R
scrnadegs.R
 
 
scrnaseqworkflow.JPG
scrnaseqworkflow.JPG
 
 
scvianalysis.ipynb
scvianalysis.ipynb
 
 
singlecell2bulkseurat.R
singlecell2bulkseurat.R
 
 
testseuratHAS.R
testseuratHAS.R
 
 
venndiagramadjusted.R
venndiagramadjusted.R
 
 

Repository files navigation

Some tips to run cellqc pipeline

  • Create simbolic links to the files ln -s

  • unzip all the .tar.gz files, and create a folder to all of them analysis.tar.gz filtered_feature_bc_matrix.tar.gz raw_feature_bc_matrix.tar.gz

  • Optional configuration for dropkick [to be tested] dropkick: skip: false method: multiotsu numthreads: 2 #INSTEAD 1

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Single cell ATAC and RNA seq data analysis

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bioinformatics-pipeline atac-seq single-cell-analysis merfish

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