markziemann Gene-function-imputation issues

markziemann / Gene-function-imputation

Gene function imputation by coexpression

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test issue

#43 megan-soria opened 11 months ago
0
cuttree_values used in Imputation & DataPrep scripts, but Imputation.rmd and Clusters.rmd are required to run before imputation blinded?

#42 casbap opened 2 years ago
0
most of these files do not exist

#41 casbap opened 2 years ago
0
non-dynamic, does not run full function without human intervention & therefore doesn't knit

#40 casbap opened 2 years ago
0
function not working under current method

#39 casbap opened 2 years ago
0
dendrogram

#38 megan-soria opened 2 years ago
0
Data prerp bug on line 278

#37 megan-soria opened 2 years ago
2
Create function to avoid the big chunks of code for the coarse sweep section in the YeastImputation-blinded.rmd

#36 megan-soria closed 3 years ago
2
Note: Using InterMine to query info for yeast

#35 megan-soria closed 3 years ago
0
[Notes]: do.call rbind behaves differently in different R versions

#34 megan-soria closed 3 years ago
1
Column dimensions not equal after blinding due to colsums > 0 filter

#33 megan-soria closed 3 years ago
2
Update the Project readme

#32 megan-soria opened 3 years ago
1
Chunk options

#31 markziemann opened 3 years ago
0
Make a function for Clustering

#30 megan-soria closed 3 years ago
1
Kfold validation

#29 megan-soria closed 3 years ago
1
Make a function that would do the analysis for a specific cluster

#28 megan-soria opened 3 years ago
0
Functions for data viz

#27 megan-soria closed 3 years ago
1
Cross validation code to check for imputation

#26 megan-soria opened 3 years ago
3
Turn intra cluster analysis into a function

#25 megan-soria closed 3 years ago
1
[Notes]: merge function

#24 megan-soria closed 3 years ago
0
[Notes]: GeneIDs in the gene count data is more than the GeneIDs in the GO matrix

#23 megan-soria closed 3 years ago
2
GO matrix genes does not match most genes in rna-seq data

#22 megan-soria closed 3 years ago
1
[Code]: How to compare elements in two vectors

#21 megan-soria closed 3 years ago
1
Create subtraction matrix for all genes in cluster 1

#20 megan-soria closed 3 years ago
1
Re-arrange rmd chunks into separate rmds

#19 megan-soria closed 3 years ago
1
Visualizations for imputation

#18 megan-soria closed 3 years ago
0
Changed the denominator of the normalization for wcorr2_cluster function

#17 megan-soria closed 3 years ago
3
Original correlation per gene in a cluster: Merge code does not have a key

#16 megan-soria closed 3 years ago
1
correlation values from hierarchical cluster was used instead of the normalized counts

#15 megan-soria closed 3 years ago
1
Data shape might be causing negatives in the subtraction matrix. Wil recheck

#14 megan-soria closed 3 years ago
2
Post imputation checklist

#13 megan-soria closed 3 years ago
1
Why are imputed GOs -1?

#12 megan-soria closed 3 years ago
6
Sophia to run example recommenderLab workflows

#11 markziemann closed 3 years ago
2
Yeast hierarchical clustering

#10 markziemann opened 4 years ago
1
Session information required

#9 markziemann closed 4 years ago
1
Too much output

#8 markziemann closed 4 years ago
1
The wide data frame needs colnames

#7 markziemann closed 4 years ago
1
Suppress package startup messages

#6 markziemann closed 4 years ago
1
Rmd header

#5 markziemann closed 4 years ago
1
location for html files

#4 markziemann closed 4 years ago
3
Directly read bz2 data

#3 markziemann closed 4 years ago
1
Begin with filtering yeast bulk data

#2 markziemann closed 4 years ago
3
Sophia to begin literature report

#1 markziemann closed 4 years ago
2