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Development #6

Merged
merged 60 commits into from
Oct 9, 2024
Merged

Development #6

merged 60 commits into from
Oct 9, 2024

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Maiykol
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@Maiykol Maiykol commented Oct 9, 2024

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@lspindler2509
first draft of pathway enrichment
a19b87b
@lspindler2509
adjusted string according to frontend
38b3bc9
@lspindler2509
parse own gene sets accordning to parameters (needed for background),…
742a904 
… filter by adjusted p-value
@lspindler2509
deleted unnecessary parameters, added background
7a737cc
@lspindler2509
always use symbol graph since genesets are based on symbol idspace
9ece308
@lspindler2509
start to parsing result, no empty string anymore in genes of geneset,…
7ab9d78 
… mapping of pathway
@lspindler2509
create networks
cc62ff3
@lspindler2509
draft on rsult output
2e32c77
@lspindler2509
added progress steps for frontend, added groups to config
e350c90
@lspindler2509
adjust config name
1944553
@lspindler2509
deleted unnecessary print
33620c1
@lspindler2509
deleted unnecessary import/logs, added drugstonetype
9c85723
@lspindler2509
added genesets in all idspaces, added odd_ratio, could delete mapping…
abf1533 
… of idspaces
@lspindler2509
only parse one pathway and when switching geneset/pathway, calculate …
c14b90d 
…chosen one
@lspindler2509
only add groups for pathway enrichment, if not availale in config
10bce46
@lspindler2509
added create_geneset api that can be called from postman etc.
2a89e16
@lspindler2509
added isSeed, adjustments in logging
6c21029
@lspindler2509
added documentation to pathway enrichment
c22fdec
@lspindler2509
different colour for overlap since previous colour already used for f…
eb197c8 
…oundNode
@lspindler2509
add edges api
04b51f5
@lspindler2509
added louvain clustering (edges not filled from ppi graph yet)
ceeac27
@lspindler2509
use distinctipy for colour coding
54941b7
@lspindler2509
deleted unnecessary import
18e6e64
@lspindler2509
add edges from interaction graph, possibility to ignore isolated node…
b21f02a 
…s in clustering
@lspindler2509
delete logs, round percentage
f6e8bbd
@lspindler2509
new group for added nodes
bedc9e6
@lspindler2509
only use chosen nodes and not whole input network
f2b960a
@lspindler2509
round odds ratio
12575db
@lspindler2509
preperations for download of pathway enrichment, clustered proteins
74202f6
@lspindler2509
add cellular component to DB
15e1343
lspindler2509 and others added 29 commits April 24, 2024 19:04
@lspindler2509
some fixes for cellular components
92a63cf
@lspindler2509
add cellular component for ensembl
5a2bd68
@lspindler2509
add layer determination
0f1c93d
@lspindler2509
map layer in backend
2c1d1a7
@lspindler2509
add layouting
c06e1ab
@lspindler2509
fixed order for layers
a3c86b1
@lspindler2509
add random layout
f06fbad
@lspindler2509
start pathway enrichment with tableview
cf9c607
@lspindler2509
added leiden clustering
420c407
@lspindler2509
added references
05fdc37
@lspindler2509
parse file in backend
cef7426
@lspindler2509
use default node group
99350a7
@lspindler2509
add default node group
6bc14a5
@lspindler2509
parse .gt files
75a6956
@lspindler2509
updated/added documentation to backend task
9724085
@lspindler2509
delete old code
64d7dc8
@lspindler2509
optional group attribute for .gt and .graphml
c2787c9
@lspindler2509
check if nodes in graph
7b646ff
@lspindler2509
added gseapy version
c182887
@lspindler2509
added versions
494663b
@Maiykol
Merge branch 'production' into development
96bb349
@lspindler2509
Merge remote-tracking branch 'upstream/development' into pathway-enri…
6855f8e 
…chment
@lspindler2509
delete old test file
b6b8ec7
@lspindler2509
adjusted import
886a907
@AndiMajore
Merge pull request #5 from lspindler2509/pathway-enrichment
5e40ebb 
Pathway enrichment
@Maiykol
Merge branch 'development' of github.com:drugst-one/backend into deve…
932d995 
…lopment
@Maiykol
revert pathway merge
bd3d3ac
@Maiykol
bugfix for custom_edges input bug
c12aa49
@Maiykol
Merge branch 'production' into development
eff19b5
@Maiykol Maiykol merged commit 20d4d63 into production Oct 9, 2024
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3 participants
@Maiykol @lspindler2509 @AndiMajore