kevinrue GOexpress-original issues

kevinrue / GOexpress-original

Original repository for Bioconductor package. Now at:

https://github.com/kevinrue/GOexpress

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issues

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ggplot dotplot

#32 kevinrue opened 9 years ago
0
Shorter vignette with example commands in addition to wordy UserGuide

#31 kevinrue opened 9 years ago
0
gene name in expression plots in italic

#30 kevinrue opened 9 years ago
0
Sample shiny app links

#29 kevinrue opened 9 years ago
0
overlap_GO: VennDiagram not detected for n=3 groups

#28 kevinrue closed 9 years ago
1
include inferential statistics (e.g. p-values)

#27 kevinrue closed 9 years ago
1
say which of rank or score was used to order the output objects

#26 kevinrue closed 9 years ago
1
Heatmap_GO: use gene_id where gene name is not available

#25 kevinrue closed 9 years ago
1
VennDiagram package required, possibly not installed in the biocLite command

#24 kevinrue closed 9 years ago
1
Include RPL36A in the toy dataset

#23 kevinrue closed 9 years ago
1
Heatmap_GO: allow relabelling of rows without affecting the color-coding of samples

#22 kevinrue closed 9 years ago
1
Include a gene with multiple Ensembl IDs in the dataset for example in the manual

#21 kevinrue closed 9 years ago
3
use the annotation file with the data set so the results can be reproduced exactly as shown in the guide?

#20 kevinrue closed 9 years ago
2
library(GOexpress) should come before you load data(AlvMac)

#19 kevinrue closed 9 years ago
1
instructions on how to generate an AnnotatedDataFrame and ExpressionSet from text files

#18 kevinrue closed 9 years ago
1
Order table_genes by rank/score

#17 kevinrue closed 9 years ago
1
Add a slot to subsetted scores describing the subsetting

#16 kevinrue closed 9 years ago
1
Tip for manual

#15 kevinrue closed 9 years ago
2
Set the bioclite code in the vignette to eval=FALSE

#14 kevinrue closed 9 years ago
1
Scoring of GO terms according to co-expression (?)

#13 kevinrue closed 9 years ago
2
Expression plot showing each individual sample colored by group

#12 kevinrue closed 10 years ago
1
heatmap/clustering using multiple GO terms?

#11 kevinrue closed 10 years ago
0
Check that the expression data is a matrix

#10 kevinrue closed 10 years ago
0
Is it desirable to alter the scoring function to reduce the bias toward GO terms with fewer genes?

#9 kevinrue closed 9 years ago
2
support microarray data

#8 kevinrue closed 10 years ago
0
expression_plot() BioMart feature missing

#7 kevinrue closed 10 years ago
0
Rename anovaGO to GOcluster

#6 kevinrue closed 10 years ago
2
A function subsetting the table of score by namespace of GO term

#5 kevinrue closed 10 years ago
3
Accelerate the step calculating all ANOVA tests

#4 kevinrue closed 10 years ago
1
a function plotting the expression profile of a given gene name

#3 kevinrue closed 10 years ago
1
A function plotting the expression profile of a given ensembl id

#2 kevinrue closed 10 years ago
1
Function to return a table describing genes related to GO_id

#1 kevinrue closed 10 years ago
0