BradhamLab scPipe issues

BradhamLab / scPipe

Pipeline for scRNAseq read alignment

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Filtering cells using a criteria met by all cells breaks functionality

#57 dakota-hawkins opened 6 years ago
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Profile `set_on_off()` to speed up.

#56 dakota-hawkins closed 6 years ago
1
Compare expression profiles

#55 dakota-hawkins opened 6 years ago
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Intelligently threshold expression profiles

#54 dakota-hawkins closed 6 years ago
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Better modularize SnakeFile

#53 dakota-hawkins opened 6 years ago
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Add Gini Coefficient when calculating HVGs

#52 dakota-hawkins closed 6 years ago
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Add TPM Support to gene collapse.

#51 dakota-hawkins opened 6 years ago
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Add 'on-off' detection using GMMs

#50 dakota-hawkins closed 6 years ago
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Add transcript length annotation to gene data

#49 dakota-hawkins opened 6 years ago
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filter genes based on drop out %

#48 dakota-hawkins closed 6 years ago
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Implement DE analysis

#47 dakota-hawkins closed 6 years ago
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Create expectation deviation plots.

#46 dakota-hawkins closed 6 years ago
1
Perform pairwise G-tests to find treatment enriched clusters.

#45 dakota-hawkins closed 6 years ago
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Project treated cells onto control UMAP. Perform louvain clustering.

#44 dakota-hawkins closed 6 years ago
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Transform informative control genes using UMAP

#43 dakota-hawkins closed 6 years ago
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Implement Cluster Analysis

#42 dakota-hawkins closed 6 years ago
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Add collapse by UniProt name

#41 dakota-hawkins closed 6 years ago
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Change log norm to log(x + 1)

#40 dakota-hawkins closed 6 years ago
1
Add TF-IDF normalization step

#39 dakota-hawkins opened 6 years ago
0
Look in to negative expression values in tpm normalized data.

#38 dakota-hawkins opened 6 years ago
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Add absolute estimation with tpm counts via monocle.

#37 dakota-hawkins closed 6 years ago
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Add TPM Normalization

#36 dakota-hawkins closed 6 years ago
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Look into BCSeq Quantification for V 0.2

#35 dakota-hawkins closed 6 years ago
1
Add variable gene extraction

#34 dakota-hawkins closed 6 years ago
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Fix Snakefiles to work with dataset: ends: nesting

#33 dakota-hawkins closed 6 years ago
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Specify expected output files exactly from STAR genome generation

#32 dakota-hawkins opened 6 years ago
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Add optional cluster 'cluster' parameter that species cluster run

#31 dakota-hawkins opened 6 years ago
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Document new configuration set up

#30 dakota-hawkins opened 6 years ago
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Document required conda environments

#29 dakota-hawkins opened 6 years ago
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Add original data protection in combined data step

#28 dakota-hawkins opened 6 years ago
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Create normalization Report

#27 dakota-hawkins opened 6 years ago
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Add configuration argument that species desired output.

#26 dakota-hawkins closed 6 years ago
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Consider `scater` for expression matrix QC

#25 dakota-hawkins closed 6 years ago
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Add plotting + reports to CountMatrix QC

#24 dakota-hawkins opened 6 years ago
1
Fix multi-columns in metadata merge.

#23 dakota-hawkins closed 6 years ago
0
Impute values using MAGIC

#22 dakota-hawkins closed 6 years ago
2
Feature/process cmatrix

#21 dakota-hawkins closed 6 years ago
0
Consider 'meta-configuration file'

#20 dakota-hawkins closed 6 years ago
0
Create separate metadata file for sample info

#19 dakota-hawkins closed 6 years ago
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Remove global variables where possible

#18 dakota-hawkins closed 6 years ago
0
Nest tool parameters in config file

#17 dakota-hawkins closed 6 years ago
1
Consider subroutine-specific environments

#16 dakota-hawkins opened 6 years ago
1
Implement Batch Assignment

#15 dakota-hawkins closed 6 years ago
0
Implement dataset merging at count matrix level

#14 dakota-hawkins closed 6 years ago
3
Implement Count Matrix QC

#13 dakota-hawkins closed 6 years ago
0
Implement sample normalization SCRAN

#12 dakota-hawkins closed 6 years ago
0
Feature/modularization

#11 dakota-hawkins closed 6 years ago
0
Make QC subroutine of alignment

#10 dakota-hawkins closed 6 years ago
0
Move all aggregate methods to parent snakefile

#9 dakota-hawkins closed 6 years ago
0
Create helper function python script

#8 dakota-hawkins closed 6 years ago
0