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Teichlab
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Pan_fetal_immune
Collection of scripts for analysis of pan fetal immune atlas
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Improved QC and annotation checklist
#52
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emdann
closed
2 years ago
emdann
commented
2 years ago
[x] PFI
[x] make raw
[x] calculate HVGs
[x] 2drive
[x] scVI
[x] emb+clustering
[x] Split and first filtering (remove mat contaminants, doublet clusters, low q samples from unusual sorts)
[x] MYELOID_NEW
[x] make raw
[x] calculate HVGs
[x] 2drive
[x] scVI
[x] emb+clustering
[x] Save QCed version
[x] LYMPHOID_NEW
[x] make raw
[x] calculate HVGs
[x] 2drive
[x] scVI
[x] emb+clustering
[x] Save QCed version
[x] STROMA_NEW
[x] make raw
[x] calculate HVGs
[x] 2drive
[x] scVI
[x] emb+clustering
[x] Save QCed version
[x] ERYTHROID_NEW
[x] make raw
[x] calculate HVGs
[x] 2drive
[x] scVI
[x] emb+clustering
[x] Save QCed version
Post QC annotation
[x] MYELOID_NEW_POSTQC
[x] calculate HVGs
[x] 2drive
[x] scVI
[x] emb+clustering
[ ] annotate
[x] LYMPHOID_NEW_POSTQC
[x] calculate HVGs
[x] 2drive
[x] scVI
[x] emb+clustering
[x] make NKT view
[ ] annotate
[x] STROMA_NEW_POSTQC
[x] calculate HVGs
[x] 2drive
[x] scVI
[x] emb+clustering
[ ] annotate
[x] ERYTHROID_NEW_POSTQC
[x] calculate HVGs
[x] 2drive
[x] scVI
[x] emb+clustering
[ ] annotate
[x] NKT_NEW_POSTQC
[x] calculate HVGs
[x] 2drive
[x] scVI
[x] emb+clustering
[ ] annotate
[x] HSC_PROGENITORS
[x] Assemble from mye/lymph/ery
[x] calculate HVGs
[x] 2drive
[x] scVI
[x] emb+clustering
[ ] HSC_PROGENITORS_POSTQC
[x] calculate HVGs
[x] 2drive
[x] scVI
[x] emb+clustering
New assembly
[ ] HSC_IMMUNE
[ ] Assemble from mye/lymph/ery
[ ] calculate HVGs
[ ] 2drive
[ ] scVI
[ ] emb+clustering
[ ] PFI_POSTQC
[ ] Assemble from mye/lymph/ery
[ ] calculate HVGs
[ ] 2drive
[ ] scVI
[ ] emb+clustering
emdann
commented
2 years ago
Improvements to implement:
[x] revised cell cycle gene list -
list
-
ref
[x] move ILCs to NKT embedding
emdann
commented
2 years ago
Post QC annotation
New assembly