markziemann mitch_legacy issues

markziemann / mitch_legacy

An R package for multi-dimensional pathway enrichment analysis (legacy repo)

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DE analysis with ascend

#69 markziemann opened 5 years ago
0
Genes by sector is too big in high dimensional data

#68 markziemann closed 5 years ago
0
Handling NAs in manova analysis

#67 markziemann closed 5 years ago
1
backwards compatibility

#66 markziemann closed 5 years ago
1
Handling NAs during import

#65 markziemann closed 5 years ago
0
Managing non-unique gene IDs

#64 markziemann closed 5 years ago
2
Taucharts is not in CRAN parhaps we should try echarts4r

#63 markziemann opened 5 years ago
6
Error in Rmd

#62 markziemann closed 5 years ago
1
Heatmap issue

#61 markziemann closed 5 years ago
0
is it possible to use all cores to speed up mitch_plots?

#60 markziemann closed 5 years ago
1
Allow user to toggle missingness tolerance

#59 markziemann closed 5 years ago
0
Import "preranked" files from unspecified upstream analysis

#58 markziemann closed 5 years ago
0
Swish and samseq

#57 markziemann closed 5 years ago
0
Webserver?

#56 markziemann closed 4 years ago
0
R CMD check yields many errors

#55 markziemann closed 5 years ago
0
Need to fix this hack

#54 markziemann closed 5 years ago
0
priority by standard deviation

#53 markziemann closed 5 years ago
1
Error with report for high dimensional analysis

#52 markziemann closed 5 years ago
1
mitch_import: cryptic error when gt is given but no geneIDcol

#51 markziemann closed 5 years ago
1
import from topconfects

#50 markziemann closed 5 years ago
0
import from muscat

#49 markziemann closed 5 years ago
1
obtain reactome gene sets

#48 markziemann closed 5 years ago
1
add option to perform 1d analysis

#47 markziemann closed 5 years ago
1
Cryptic error when DEtype is incorrectly set

#46 markziemann closed 5 years ago
0
Make sure gplots is required for installation

#45 markziemann closed 5 years ago
1
mcinteractive package...

#44 markziemann closed 5 years ago
2
in the html report, the analysis is still called nDrichr

#43 markziemann closed 5 years ago
1
Add gene names to the 2D plots

#42 markziemann opened 5 years ago
1
Knitr dies when looking for confESp when bootstrapping not performed

#41 markziemann closed 5 years ago
1
Mitch ggplot dies when colname begins with a number

#40 markziemann closed 5 years ago
1
Save version info to outputs

#39 markziemann closed 5 years ago
1
RMD should be downloaded to tmpfile

#38 markziemann closed 5 years ago
0
Bug with naming genesets

#37 markziemann closed 5 years ago
0
include a heatmap of top gene sets in the pdf and html

#36 markziemann closed 5 years ago
1
GGplot2 error subscript out of bounds

#35 markziemann closed 5 years ago
2
Implement setRank procedure

#34 markziemann opened 5 years ago
1
Colour-code the vioplot to indicate the s.dist

#33 markziemann closed 5 years ago
3
Need some documentation

#32 markziemann closed 5 years ago
0
Test

#31 markziemann closed 5 years ago
2
Bug with bootstraps

#30 markziemann closed 5 years ago
0
4d PDF and Rmd errors

#29 markziemann closed 5 years ago
1
Make R package

#28 markziemann closed 5 years ago
0
There are some formatting issues with the Rmd

#27 markziemann closed 5 years ago
1
Support resrows larger than num genesets

#26 markziemann closed 5 years ago
1
Bootstrapping to generate confidence intervals of the s statistic

#25 markziemann closed 5 years ago
3
The PDF and Markdown output needs a plot of ES vs -log10(FDR)

#24 markziemann closed 5 years ago
1
Need some comparison of significance and effect size

#23 markziemann closed 5 years ago
2
The PDF output needs a scatterplot of pathways

#22 markziemann closed 5 years ago
1
Rmd error

#21 markziemann closed 5 years ago
1
Function to import contrast data from commonly used differential tools edgeR, limma, sleuth, DESeq and other

#20 markziemann closed 5 years ago
1