epigen scrnaseq_processing_seurat issues

epigen / scrnaseq_processing_seurat

A Snakemake workflow for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix file format powered by the R package Seurat.

MIT License

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misc enhancements

#25 sreichl closed 5 hours ago
0
Handle exception when genes not found in data

#24 sreichl closed 6 hours ago
0
support h5ad as input format

#23 sreichl opened 1 month ago
0
adapt heatmap width when downsampling acccordingly

#22 sreichl closed 6 hours ago
0
document parse bioscience data conversion to compatible mtx format

#21 sreichl opened 5 months ago
0
full tests on new functions

#20 sreichl closed 7 months ago
0
update documentation

#19 sreichl closed 7 months ago
0
extend pseudobulking functionality

#18 sreichl closed 7 months ago
0
add example data

#17 sreichl closed 7 months ago
0
restructure results and speed up plotting

#16 sreichl closed 7 months ago
3
speed up rule save_counts (bottleneck)

#15 sreichl closed 7 months ago
1
order all plot panels alphabetical

#14 sreichl closed 7 months ago
0
make normalization configurable

#13 sreichl opened 9 months ago
0
dynamic memory for data intense rules depending on input

#12 sreichl closed 7 months ago
0
extend KOcall strategy beyond singlets

#11 sreichl closed 7 months ago
1
Cyclic graph dependency when metadata not provided

#10 sreichl closed 9 months ago
0
generalize to other modalities e.g., sc/snATAC-seq

#9 sreichl closed 5 hours ago
1
background noise removal using CellBender

#8 sreichl opened 1 year ago
1
pseudobulking of counts by metadata feature

#7 sreichl closed 7 months ago
0
make dot plot color scale centered at 0

#6 sreichl closed 7 months ago
0
update to sctransform to use vst.flavor="v2"

#5 sreichl closed 7 months ago
0
all heatmaps should be hierarchically clustered eg using hclust

#4 sreichl closed 7 months ago
0
add support for generic gene by barcode/cell count matrices

#3 sreichl closed 2 years ago
0
add support for additional metadata file emerged from downstream analyses

#2 sreichl closed 2 years ago
1
save result object in h5ad format for better interoperability with other packages

#1 sreichl opened 2 years ago
2