naikai sake issues - Githubissues

naikai / sake

sake

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Option to download data by NMF groups

#34 naikai closed 8 years ago
1
Add option to color samples by gene expression value in t-SNE or PCA plot

#33 naikai closed 8 years ago
1
Need to add option to normalize data by ERCC spike-in

#32 naikai opened 8 years ago
0
Generate box plot for DESeq results with a download button

#31 naikai closed 7 years ago
0
Import download function for heatmap

#30 naikai closed 8 years ago
1
Add options to run NMF from cluster and import back the results to shiny

#29 naikai closed 7 years ago
6
Updated README for required components on an average tool: Info Box, …

#28 molikd closed 8 years ago
0
Can't download NMF "estimate number of k's" data

#27 taicher closed 8 years ago
1
datatable is not downloading all the data

#26 naikai closed 8 years ago
0
Add gene network topology for feature selection

#25 naikai opened 8 years ago
3
Pressing delete quit program

#24 taicher closed 8 years ago
1
DESeq module should always use raw count even if we transformed the data

#23 naikai closed 8 years ago
2
Add download button back for transformed data

#22 naikai closed 8 years ago
1
Add descriptions for each of the NMF options

#21 naikai closed 8 years ago
1
highlight NMF identified genes in DESeq2 results

#20 naikai closed 7 years ago
0
NMF group assignments don't match between nmf_groups and (DESeq2 or Enrichment analysis)

#19 naikai closed 8 years ago
1
Transformation and Correlation will become super slow if sample size is large (>= 1000)

#18 naikai closed 8 years ago
2
Add seed option for NMF

#17 naikai closed 8 years ago
1
Add p-value graph for GO-term results

#16 naikai closed 7 years ago
1
App option to use logFC from DESeq results for Pathway analysis

#15 naikai opened 8 years ago
0
Clean up t-SNE plot after changing the gene sets

#14 naikai closed 7 years ago
1
shiny loading time increases with plotly

#13 naikai closed 8 years ago
1
Save plotly graphs in Shiny

#12 naikai closed 8 years ago
4
Coupled events in plotly charts using Shiny

#11 naikai closed 8 years ago
1
Errors installing package on travis

#10 naikai opened 8 years ago
0
8 nodes produced errors; first error: Remove duplicates before running TSNE

#9 naikai closed 8 years ago
2
KEGG should display error when feed other than human gene count

#8 naikai closed 8 years ago
1
NMF estim and real switch will cause problem for featureScore

#7 naikai closed 8 years ago
2
Add DESeq2 options in the sidetab

#6 naikai closed 8 years ago
2
Add WGCNA as gene filtering step

#5 naikai closed 7 years ago
0
Add log option for scatter plot

#4 naikai closed 8 years ago
1
Add small Correlation plot for ‘Filter gene list’

#3 naikai closed 8 years ago
1
t-SNE plot for NMF group

#2 naikai closed 8 years ago
3
Add ColSideColor in heatmap based on NMF results

#1 naikai closed 8 years ago
1