Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / stephenslab/fastTopics issues and pull requests

#59 - Question about feature selection

Issue - State: closed - Opened by AmosFong1 25 days ago - 2 comments

#58 - Recommendations for performing GSEA on topics?

Issue - State: open - Opened by AmosFong1 27 days ago - 3 comments

#57 - Segmentation fault in de_analysis with nc > 1

Issue - State: closed - Opened by aksarkar 2 months ago - 6 comments
Labels: bug

#56 - Improve multithreading in fit_poisson_nmf

Issue - State: open - Opened by pcarbo 3 months ago - 4 comments

#55 - Usage of fastTopics for multi condition multi timepoints datasets

Issue - State: open - Opened by JonasDBM 7 months ago - 2 comments

#54 - Improve documentation of nc control parameter

Pull Request - State: closed - Opened by aksarkar 10 months ago - 1 comment

#53 - Reduce memory usage in compute_lfc_stats_multicore

Pull Request - State: open - Opened by aksarkar 11 months ago - 2 comments

#52 - Improve multithread DE analysis

Pull Request - State: closed - Opened by aksarkar 11 months ago - 3 comments

#51 - Report how many threads are being used in fit_poisson_nmf

Pull Request - State: closed - Opened by aksarkar 11 months ago - 1 comment

#50 - Segmentation fault in multithreading setup

Issue - State: open - Opened by aksarkar 11 months ago - 8 comments
Labels: bug

#48 - Feature request: early stopping

Issue - State: closed - Opened by aksarkar 11 months ago - 5 comments

#47 - Considerations for bulk RNAseq

Issue - State: closed - Opened by kayserb 11 months ago - 2 comments

#46 - Add website to DESCRIPTION

Pull Request - State: closed - Opened by olivroy about 1 year ago - 3 comments

#45 - Allow "fit" argument to structure_plot to also be an "L" matrix, similar to de_analysis.

Issue - State: open - Opened by pcarbo about 1 year ago - 1 comment
Labels: enhancement

#43 - Add more colors to structure_plot

Issue - State: closed - Opened by pcarbo over 1 year ago - 2 comments
Labels: enhancement

#42 - Type I error control for homogenous case

Issue - State: closed - Opened by william-denault over 1 year ago - 2 comments

#41 - fastTopics on normalized data

Issue - State: open - Opened by nesilin over 1 year ago - 3 comments

#40 - A question on the paper on differentiation expression

Issue - State: open - Opened by Chengwei94 over 1 year ago - 3 comments

#39 - Improve documentation for parallel computing options

Issue - State: closed - Opened by aksarkar over 1 year ago - 10 comments

#38 - Flip columns of X in poisson2binom (branch:poisson2binom)

Issue - State: open - Opened by pcarbo over 1 year ago

#37 - de_analysis save intermediate steps + return likelihood optimization requests

Issue - State: closed - Opened by MarcElosua almost 2 years ago - 19 comments

#36 - de_analysis using LDA Topic Modeling

Issue - State: closed - Opened by gomeznick86 almost 2 years ago - 6 comments

#35 - Feature request: multi-threaded DE analysis

Issue - State: open - Opened by aksarkar almost 2 years ago - 14 comments

#34 - Curious about how fast is the CD algorithm compared to SQUAREM

Issue - State: closed - Opened by Zilong-Li almost 2 years ago - 2 comments

#33 - Contract topics feature

Issue - State: closed - Opened by UboCA almost 2 years ago - 2 comments

#32 - diff_count_clusters not found

Issue - State: closed - Opened by NicoloPecco about 2 years ago - 6 comments

#31 - function error-diff_count_clusters() & diff_count_analysis()

Issue - State: closed - Opened by geng-lee over 2 years ago - 2 comments

#30 - Geting Help for FastTopics Error

Issue - State: closed - Opened by geng-lee over 2 years ago - 5 comments

#29 - Update Vignette

Issue - State: closed - Opened by nikofleischer over 2 years ago - 2 comments

#28 - bug in compile_structure_plot_data when a group is empty

Issue - State: closed - Opened by willwerscheid almost 3 years ago - 3 comments

#27 - Feature request: Gamma prior for NMF loadings

Issue - State: closed - Opened by jackkamm almost 3 years ago - 6 comments

#26 - Feature request: Batch correction variable?

Issue - State: closed - Opened by dagarfield almost 3 years ago - 8 comments

#25 - Fix quiet output

Pull Request - State: closed - Opened by aksarkar almost 3 years ago - 1 comment

#24 - count not find function "diff_count_clusters"

Issue - State: closed - Opened by guanxn90 almost 3 years ago - 2 comments

#23 - Threading init message is printed even when verbose="none"

Issue - State: closed - Opened by aksarkar almost 3 years ago - 1 comment
Labels: bug

#22 - structure_plot not working on "fit" from "predict()" function

Issue - State: closed - Opened by Zepeng-Mu about 3 years ago - 6 comments

#21 - RcppParallel library flags

Issue - State: closed - Opened by YPARK over 3 years ago - 3 comments

#20 - Convergence issues?

Issue - State: closed - Opened by cnk113 over 3 years ago - 5 comments

#19 - handling large datasets

Issue - State: closed - Opened by tomthomas3000 over 3 years ago - 10 comments

#18 - More gracefully handle error in structure_plot when there are not enough colours

Issue - State: closed - Opened by pcarbo over 3 years ago
Labels: bug

#17 - Extracting all the genes for a given topic AND how to change volcano plot

Issue - State: closed - Opened by maxybck over 3 years ago - 2 comments

#16 - Improve documentation for fit_topic_model

Issue - State: open - Opened by pcarbo over 3 years ago

#15 - Properly handle count matrices with all-zero rows

Issue - State: open - Opened by pcarbo over 3 years ago

#14 - Suggestions/questions about output

Issue - State: closed - Opened by willwerscheid over 3 years ago - 18 comments
Labels: bug

#13 - Imported Count Matrix by Seurat, but Col Names are Cell Names

Issue - State: closed - Opened by h1hui almost 4 years ago - 2 comments

#12 - feedback on structure_plot

Issue - State: closed - Opened by stephens999 almost 4 years ago - 9 comments
Labels: enhancement

#11 - Create vignette to illustrate "projection" of samples onto existing F matrix

Issue - State: closed - Opened by pcarbo almost 4 years ago
Labels: enhancement

#10 - Naming in a structure_plot for small number of samples

Issue - State: closed - Opened by maxybck almost 4 years ago - 5 comments

#9 - Extract top genes for each topic

Issue - State: closed - Opened by chendianyu almost 4 years ago - 1 comment

#8 - Computing topics over normalized data

Issue - State: closed - Opened by GreenGilad almost 4 years ago - 8 comments

#7 - Convergence test and input count matrix

Issue - State: closed - Opened by satriaps about 4 years ago - 3 comments
Labels: enhancement

#6 - Installation issues

Issue - State: closed - Opened by l-cli about 4 years ago - 3 comments

#5 - Take care of warning, "Quick-TRANSfer stage steps exceeded maximum"

Issue - State: open - Opened by pcarbo over 4 years ago
Labels: bug

#4 - Implement function to estimate loadings in held-out samples

Issue - State: open - Opened by pcarbo over 4 years ago
Labels: enhancement

#3 - fit_poisson_nmf Error in solve.QP(M, d, A, b0)

Issue - State: closed - Opened by jhsiao999 almost 5 years ago - 5 comments
Labels: bug

#2 - fit_poisson_nmf error with k=2

Issue - State: closed - Opened by jhsiao999 almost 5 years ago - 1 comment