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stephenslab
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fastTopics
Fast algorithms for fitting topic models and non-negative matrix factorizations to count data.
https://stephenslab.github.io/fastTopics
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Usage of fastTopics for multi condition multi timepoints datasets
#55
JonasDBM
opened
1 month ago
2
Improve documentation of nc control parameter
#54
aksarkar
closed
5 months ago
1
Reduce memory usage in compute_lfc_stats_multicore
#53
aksarkar
opened
5 months ago
2
Improve multithread DE analysis
#52
aksarkar
closed
5 months ago
3
Report how many threads are being used in fit_poisson_nmf
#51
aksarkar
closed
5 months ago
1
Segmentation fault in multithreading setup
#50
aksarkar
opened
5 months ago
8
What is a sensible threshold to select the most informative features per topic?
#49
massonix
closed
5 months ago
2
Feature request: early stopping
#48
aksarkar
closed
5 months ago
5
Considerations for bulk RNAseq
#47
kayserb
closed
6 months ago
2
Add website to DESCRIPTION
#46
olivroy
closed
7 months ago
3
Allow "fit" argument to structure_plot to also be an "L" matrix, similar to de_analysis.
#45
pcarbo
opened
7 months ago
1
Error in verify.fit.and.count.matrix(X, fit) : Dimensions of input matrices "X" , "fit$F" and "fit$L" do not agree
#44
ZhengYingqi-doctor
opened
7 months ago
4
Add more colors to structure_plot
#43
pcarbo
closed
12 months ago
2
Type I error control for homogenous case
#42
william-denault
closed
1 year ago
2
fastTopics on normalized data
#41
nesilin
opened
1 year ago
3
A question on the paper on differentiation expression
#40
Chengwei94
opened
1 year ago
3
Improve documentation for parallel computing options
#39
aksarkar
closed
5 months ago
10
Flip columns of X in poisson2binom (branch:poisson2binom)
#38
pcarbo
opened
1 year ago
0
de_analysis save intermediate steps + return likelihood optimization requests
#37
MarcElosua
closed
1 year ago
19
de_analysis using LDA Topic Modeling
#36
gomeznick86
closed
1 year ago
6
Feature request: multi-threaded DE analysis
#35
aksarkar
opened
1 year ago
14
Curious about how fast is the CD algorithm compared to SQUAREM
#34
Zilong-Li
closed
1 year ago
2
diff_count_clusters not found
#32
NicoloPecco
closed
1 year ago
6
function error-diff_count_clusters() & diff_count_analysis()
#31
geng-lee
closed
1 year ago
2
Geting Help for FastTopics Error
#30
geng-lee
closed
1 year ago
5
Update Vignette
#29
nikofleischer
closed
1 year ago
2
bug in compile_structure_plot_data when a group is empty
#28
willwerscheid
closed
2 years ago
3
Feature request: Gamma prior for NMF loadings
#27
jackkamm
closed
2 years ago
6
Feature request: Batch correction variable?
#26
dagarfield
closed
2 years ago
8
Fix quiet output
#25
aksarkar
closed
2 years ago
1
count not find function "diff_count_clusters"
#24
guanxn90
closed
2 years ago
2
Threading init message is printed even when verbose="none"
#23
aksarkar
closed
2 years ago
1
structure_plot not working on "fit" from "predict()" function
#22
Zepeng-Mu
closed
2 years ago
6
RcppParallel library flags
#21
YPARK
closed
2 years ago
3
Convergence issues?
#20
cnk113
closed
3 years ago
5
handling large datasets
#19
tomthomas3000
closed
3 years ago
10
More gracefully handle error in structure_plot when there are not enough colours
#18
pcarbo
closed
7 months ago
0
Extracting all the genes for a given topic AND how to change volcano plot
#17
maxybck
closed
1 year ago
2
Improve documentation for fit_topic_model
#16
pcarbo
opened
3 years ago
0
Properly handle count matrices with all-zero rows
#15
pcarbo
opened
3 years ago
0
Suggestions/questions about output
#14
willwerscheid
closed
1 year ago
18
Imported Count Matrix by Seurat, but Col Names are Cell Names
#13
h1hui
closed
3 years ago
2
feedback on structure_plot
#12
stephens999
closed
1 year ago
9
Create vignette to illustrate "projection" of samples onto existing F matrix
#11
pcarbo
closed
3 years ago
0
Naming in a structure_plot for small number of samples
#10
maxybck
closed
1 year ago
5
Extract top genes for each topic
#9
chendianyu
closed
3 years ago
1
Computing topics over normalized data
#8
GreenGilad
closed
3 years ago
8
Convergence test and input count matrix
#7
satriaps
closed
5 months ago
3
Installation issues
#6
l-cli
closed
3 years ago
3
Take care of warning, "Quick-TRANSfer stage steps exceeded maximum"
#5
pcarbo
opened
4 years ago
0
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