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epigen
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scrnaseq_processing_seurat
A Snakemake workflow and MrBiomics module 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.
https://epigen.github.io/scrnaseq_processing_seurat/
MIT License
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v3.0.0
#26
sreichl
closed
1 week ago
0
misc enhancements
#25
sreichl
closed
1 month ago
0
Handle exception when genes not found in data
#24
sreichl
closed
1 month ago
0
support h5ad as input format
#23
sreichl
opened
3 months ago
0
adapt heatmap width when downsampling acccordingly
#22
sreichl
closed
1 month ago
0
document parse bioscience data conversion to compatible mtx format
#21
sreichl
closed
1 week ago
0
full tests on new functions
#20
sreichl
closed
9 months ago
0
update documentation
#19
sreichl
closed
9 months ago
0
extend pseudobulking functionality
#18
sreichl
closed
9 months ago
0
add example data
#17
sreichl
closed
9 months ago
0
restructure results and speed up plotting
#16
sreichl
closed
9 months ago
3
speed up rule save_counts (bottleneck)
#15
sreichl
closed
9 months ago
1
order all plot panels alphabetical
#14
sreichl
closed
9 months ago
0
make normalization configurable
#13
sreichl
opened
11 months ago
0
dynamic memory for data intense rules depending on input
#12
sreichl
closed
9 months ago
0
extend KOcall strategy beyond singlets
#11
sreichl
closed
9 months ago
1
Cyclic graph dependency when metadata not provided
#10
sreichl
closed
11 months ago
0
generalize to other modalities e.g., sc/snATAC-seq
#9
sreichl
closed
1 month ago
1
background noise removal using CellBender
#8
sreichl
opened
1 year ago
1
pseudobulking of counts by metadata feature
#7
sreichl
closed
9 months ago
0
make dot plot color scale centered at 0
#6
sreichl
closed
9 months ago
0
update to sctransform to use vst.flavor="v2"
#5
sreichl
closed
9 months ago
0
all heatmaps should be hierarchically clustered eg using hclust
#4
sreichl
closed
9 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
closed
1 week ago
2