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ucscXena
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xena-analysis-grails
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added docker file
#50
nathandunn
closed
3 years ago
0
create server docker file
#49
nathandunn
opened
3 years ago
0
add admin screen (in web) to change names and make public for admin (can use HS256)
#48
nathandunn
closed
3 years ago
0
verify signed RS256
#47
nathandunn
closed
3 years ago
0
fixes-#39
#46
nathandunn
closed
3 years ago
0
basic server-side authentication trial
#45
nathandunn
closed
3 years ago
0
upload TCGA geneset again
#44
nathandunn
closed
3 years ago
0
fixes #16
#43
nathandunn
closed
3 years ago
0
find global mean and stdev for activity z-scores
#42
nathandunn
closed
3 years ago
0
fork processes based on # of processors / 2 with a minimum of 1
#41
nathandunn
closed
3 years ago
0
build out analysis server in EC2
#40
nathandunn
opened
3 years ago
0
authenticate grails server with GitHub - so users only see what they are doing and only allow some to do upload
#39
nathandunn
closed
3 years ago
18
add delete gmt
#38
nathandunn
closed
3 years ago
0
convert default BPA Geneset to GMT
#37
nathandunn
closed
3 years ago
3
fix key not found for the largest genesets
#36
nathandunn
opened
3 years ago
0
start to handle re-order for all samples
#35
nathandunn
closed
3 years ago
1
fix sample order for ALL pathways
#34
nathandunn
closed
3 years ago
0
ignores first line of the uploaded GMT
#33
nathandunn
closed
3 years ago
0
when processing the "names" field seems to disappear for a moment
#32
nathandunn
closed
3 years ago
0
mostly working to do as batch
#31
nathandunn
closed
3 years ago
0
need to add local raw gene expression back (tabs) for BPA analysis
#30
nathandunn
closed
3 years ago
0
speed up "names" method
#29
nathandunn
closed
3 years ago
0
calculate per-gene pathway analysis
#27
nathandunn
closed
3 years ago
0
added calculation method for status
#26
nathandunn
closed
3 years ago
0
create tpm z-normalized tpm files
#25
nathandunn
closed
3 years ago
0
calculate TPM per geneset
#24
nathandunn
closed
3 years ago
0
calculate per-gene pathway activity per GMT
#23
nathandunn
closed
3 years ago
0
handle SAMPLE lists for calculation of pathway and gene expression (probably done) scores
#28
nathandunn
closed
3 years ago
0
speed up results for large pathways (cache, filter)?
#22
nathandunn
opened
3 years ago
2
optimize batch upload speed
#21
nathandunn
closed
3 years ago
0
begin refactoring
#20
nathandunn
closed
3 years ago
9
allow processing of ALL Cohorts for a GMT
#19
nathandunn
closed
3 years ago
0
should properly store and return GMT files
#18
nathandunn
closed
3 years ago
0
store geneset count
#17
nathandunn
closed
3 years ago
0
pull down more proper go slims and analyze
#16
nathandunn
closed
3 years ago
5
eadded test workflow
#15
nathandunn
closed
3 years ago
0
mostly put together correctly
#14
nathandunn
closed
3 years ago
0
generate tpm download should use post
#13
nathandunn
closed
3 years ago
0
server-side github actions
#12
nathandunn
closed
3 years ago
0
fix zsample score
#11
nathandunn
closed
3 years ago
5
fix validation error - upload client-analysis versus server analysis
#10
nathandunn
closed
3 years ago
8
verify changing GMT with partial sub cohorts (detect difference)
#9
nathandunn
closed
3 years ago
0
changing GMT and cohort should and changing back should evaluate properly
#8
nathandunn
closed
3 years ago
1
changing GMT should not re-evaluate
#7
nathandunn
closed
3 years ago
0
allow change of sub cohorts for custom gene sets for upload and server-side analysis
#6
nathandunn
closed
3 years ago
0
started refactor of analysis service to minimize IO
#5
nathandunn
closed
3 years ago
1
Add postgresql 2
#4
nathandunn
closed
3 years ago
0
do output analysis on the server
#3
nathandunn
closed
3 years ago
0
support larger files: move to postgresql to support inserting more data or give H2 more memory or use File-system
#2
nathandunn
closed
3 years ago
0