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AllenInstitute
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transcriptomic_clustering
improved clustering pipeline for transcriptomic data
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Add Annoy ANN Algorithm to Forked Phenograph Code
#87
JakeSAI
closed
3 years ago
1
Make Louvain Clustering Seedable
#86
JakeSAI
closed
3 years ago
1
dataframe means in cluster means
#85
JakeSAI
closed
3 years ago
0
Merging Summary Statistics
#84
madiganz
opened
3 years ago
1
Caching of Differential Expressed Genes
#83
madiganz
opened
3 years ago
1
Add merge module
#82
madiganz
closed
3 years ago
2
Cluster means as dataframes in merging and hclust
#81
JakeSAI
closed
3 years ago
0
61 Create Chi-sq differential expression calculation
#80
gnayuy
closed
3 years ago
0
Add nearest neighbor calculation for merging
#79
madiganz
closed
3 years ago
0
Updates cluster similarity calculation to use dataframe of cluster means
#78
JakeSAI
closed
3 years ago
0
adds LICENSE, CONTRIBUTING, github templates, etc
#77
MatthewAitken
closed
3 years ago
0
adds new demo notebook for June
#76
MatthewAitken
closed
3 years ago
1
handles case if known modes is series
#75
MatthewAitken
closed
3 years ago
0
Prepare demonstration
#74
wbwakeman
closed
3 years ago
2
Add contribution guidelines to tx_clustering repo
#73
wbwakeman
closed
3 years ago
1
BLAS environment handling documentation
#72
JakeSAI
opened
3 years ago
0
Handle duplicate genes
#71
JakeSAI
opened
3 years ago
0
Document AnnData.X type requirements
#70
JakeSAI
opened
3 years ago
0
Adds chunked calculation of cluster means
#69
madiganz
closed
3 years ago
3
Bugfix/negative cluster fix
#68
JakeSAI
closed
3 years ago
2
GH-62 Add merging small clusters
#67
sgratiy
closed
3 years ago
0
fixes projection bugs with pcs dataframe
#66
MatthewAitken
closed
3 years ago
0
Update demo notebook with completed modules
#65
wbwakeman
closed
3 years ago
0
Adds UPGMA hierarchical clustering
#64
madiganz
closed
3 years ago
2
10 filter known modes
#63
gnayuy
closed
3 years ago
0
Simple Merging of small clusters
#62
MatthewAitken
closed
3 years ago
0
Create Chi-sq differential expression calculation
#61
MatthewAitken
closed
3 years ago
0
Create Limma Differential Expression function
#60
MatthewAitken
closed
3 years ago
0
fixes bug with filebacked but not chunked
#59
MatthewAitken
closed
3 years ago
0
Notebook demonstrated on May 4 2021
#58
sgratiy
closed
3 years ago
0
adds git-lfs to circleci
#57
MatthewAitken
closed
3 years ago
0
Feature/louvain
#56
JakeSAI
closed
3 years ago
1
memory cherrypick
#55
MatthewAitken
closed
3 years ago
0
adds pca
#54
MatthewAitken
closed
3 years ago
0
Fix bug with slicing of file-backed object
#53
wbwakeman
closed
3 years ago
1
Pca
#52
MatthewAitken
closed
3 years ago
0
Demo chunksizeest bugfix
#51
gnayuy
closed
3 years ago
0
simple projection module
#50
MatthewAitken
closed
3 years ago
0
update chunk size est
#49
gnayuy
closed
3 years ago
0
GH-39 Add chunked normalization for file-backed data
#48
sgratiy
closed
3 years ago
1
Demo misc
#47
sgratiy
closed
3 years ago
1
Bugfix/test memory
#46
MatthewAitken
closed
3 years ago
0
Demo filter genes and hvgs
#45
gnayuy
closed
3 years ago
0
Pca
#44
MatthewAitken
closed
3 years ago
0
39/chunk normalization
#43
sgratiy
closed
3 years ago
0
adds memory error if chunking nonfilebacked anndata
#42
MatthewAitken
closed
3 years ago
0
37 Create a threshold filtering function to filter genes based on expression
#41
gnayuy
closed
3 years ago
0
chunked normalization prototype wip
#40
sgratiy
closed
3 years ago
0
Apply chunking to normalization module
#39
wbwakeman
closed
3 years ago
0
tx clustering demo preparation, presentation, feedback
#38
wbwakeman
closed
3 years ago
1
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