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jokergoo
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simplifyEnrichment
Simplify functional enrichment results
https://jokergoo.github.io/simplifyEnrichment
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Error in running `GO_similarity`
#59
kanekalla
opened
3 years ago
2
Word cloud: show most over-represented words, not the most frequent ones
#58
krassowski
closed
2 years ago
1
Allow users to customize the count_words behaviour
#57
krassowski
closed
3 years ago
5
Word clouds based on member (gene) descriptions
#56
krassowski
closed
2 years ago
4
Colour the same words with the same colour
#55
krassowski
closed
3 years ago
1
Make the default colors colour-blind tolerable
#54
krassowski
closed
3 years ago
2
All two-letter gene/protein/metabolite names are disregarded
#53
krassowski
closed
3 years ago
1
Preserve whitespace for selected phrases and/or allow to include n-grams
#52
krassowski
closed
3 years ago
0
Review the stopwords exclusion
#51
krassowski
closed
3 years ago
0
Preserve letter case for selected words in anno_word_cloud
#50
krassowski
closed
3 years ago
0
Generic simplifyGOFromMultipleLists for gene sets databases other than GO?
#49
krassowski
opened
3 years ago
2
Installation error
#48
urjaswita
opened
3 years ago
1
add a new vignette of how to visualize GO from multiple lists
#47
jokergoo
closed
3 years ago
0
simplifyGO() function doesn't work anymore
#46
chriselhadi
closed
3 years ago
0
test the runtime for similarity matrices with different size
#45
jokergoo
closed
3 years ago
0
cache argument in binary_cut is not used
#44
jokergoo
closed
3 years ago
0
Do not generate the complete dendrogram
#43
jokergoo
closed
3 years ago
0
print more informative message if the format is wrong
#42
jokergoo
closed
3 years ago
0
Error: None of the keys entered are valid keys for 'GOID'
#41
anabbi
closed
3 years ago
5
How to customize and modify the plot from simplifyGO function?
#40
Dongxu-Zheng
closed
3 years ago
6
Implement anno_word_cloud
#39
jokergoo
closed
3 years ago
0
Error when all cluster size are smaller than the cutoff
#38
jokergoo
closed
3 years ago
0
Custom font and background color for word cloud
#37
chiayic
closed
3 years ago
2
Can this package be applied to scRNA-seq or scATAC-seq?
#36
eleozzr
closed
3 years ago
2
Custom color ramp for simplifyGO() ?
#35
dpleone
closed
3 years ago
1
in supplementary, check the value from Resnik
#34
jokergoo
closed
4 years ago
0
stop clustering when s < cutoff
#33
jokergoo
closed
3 years ago
0
partition_by_pam
#32
jokergoo
closed
4 years ago
0
allows list of GO ids as input
#31
jokergoo
closed
4 years ago
0
improve it!
#30
jokergoo
closed
4 years ago
0
This is awesome!
#29
anfederico
closed
3 years ago
1
compare_similarity(): add pairwise scatterplot
#28
jokergoo
closed
4 years ago
0
run select_cutoff()
#27
jokergoo
closed
4 years ago
0
ht_clusters(): order of clusters should be adjusted
#26
jokergoo
closed
4 years ago
0
ht_cluster(): first page is empty if saved as pdf
#25
jokergoo
closed
4 years ago
0
how to get the number of genes in a certain GO
#24
jokergoo
closed
4 years ago
0
Implement weighted jaccard/dice...
#23
jokergoo
closed
4 years ago
1
Test dice coef
#22
jokergoo
closed
4 years ago
2
try running select_cutoff for different datasets
#21
jokergoo
closed
4 years ago
0
order of cl
#20
jokergoo
closed
4 years ago
1
check MCL method
#19
jokergoo
closed
4 years ago
0
in compare methods, cluster labels should be adjusted
#18
jokergoo
closed
4 years ago
0
difference score for different partition method
#17
jokergoo
closed
4 years ago
0
cluster = 0 for hdbscan
#16
jokergoo
closed
4 years ago
0
test the stability of binary cut
#15
jokergoo
closed
4 years ago
1
plot_binary_cut and simplifyGO, the classification/plot is different?
#14
jokergoo
closed
4 years ago
0
draw the heatmap without splitting, later lines are aded by decorate...
#13
jokergoo
closed
4 years ago
0
classification needs to be confirmed by UMAP on the similarity matrix
#12
jokergoo
closed
4 years ago
0
test with more ontologies
#11
jokergoo
closed
4 years ago
3
compare different clustering results
#10
jokergoo
closed
4 years ago
0
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