Ecosyste.ms: Issues

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GitHub / helenalc/muscat issues and pull requests

#139 - polishing pbDD vignette

Pull Request - State: closed - Opened by jgilis 28 days ago - 1 comment

#138 - latent variables

Issue - State: open - Opened by Flu09 2 months ago

#137 - Problems with RNA ambient

Issue - State: closed - Opened by hahmu 3 months ago - 2 comments

#136 - pbDS(pb, design = mm, contrast = contrast) error

Issue - State: open - Opened by Jadeapple 5 months ago - 2 comments

#135 - aggregateData does not return colData

Issue - State: closed - Opened by Nayrouz109 5 months ago - 2 comments

#134 - Multiple Random Effects

Issue - State: open - Opened by jgockley62 6 months ago - 4 comments

#133 - I cannot compute pbHeatmap

Issue - State: open - Opened by bkheira 8 months ago - 2 comments

#132 - Loss of clusters during pbDS

Issue - State: closed - Opened by bkheira 8 months ago - 3 comments

#131 - Doubt in sim_mean and ground truth

Issue - State: open - Opened by cakeinspace 10 months ago - 1 comment

#128 - Error installing muscat

Issue - State: closed - Opened by MJGGaray 12 months ago - 1 comment

#127 - How is the AveExpr in mmDS calculated?

Issue - State: open - Opened by Lila3141 about 1 year ago

#126 - limma voom cpm values

Issue - State: open - Opened by AnjaliC4 about 1 year ago

#125 - DP simulated data has inverted logFC and only one bimodal group

Issue - State: open - Opened by ChristophH about 1 year ago - 3 comments

#124 - aggregateData returns all zero when there is only 1 sample_id

Issue - State: closed - Opened by jsialar over 1 year ago - 1 comment

#123 - Doubt in terminology

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

#122 - How to correct batch effects when using muscat?

Issue - State: closed - Opened by ChenyuZhang97 over 1 year ago - 2 comments

#121 - pbHeatmap y %in% assayNames(x) is not TRUE

Issue - State: closed - Opened by amoyguang1 over 1 year ago - 8 comments

#120 - muscat_analysis don't accept DICE annotation

Issue - State: closed - Opened by obotman over 1 year ago - 15 comments

#118 - Specifying contrasts in MUSCAT mixed models

Issue - State: open - Opened by ismailelshimy over 1 year ago - 6 comments

#117 - How to do sth like contrast for cell level DE analysis

Issue - State: open - Opened by pariaaliour over 1 year ago - 2 comments

#116 - res <- pbDS(pb, verbose = FALSE) Error in x[[1]] : subscript out of bounds

Issue - State: closed - Opened by Jungkooklove0901 almost 2 years ago - 3 comments

#115 - Error using aggregateData with example_sce

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

#114 - MUSCAT Mixed Effects Models and the Cellular Detection Rate

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

#113 - A constraint that might not be required in PrepSim

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

#112 - norm in limma trend

Pull Request - State: closed - Opened by XikunHan almost 2 years ago

#111 - mm_glmm("nbinom") returns NAs

Issue - State: open - Opened by Nayrouz109 about 2 years ago

#110 - mmDS() and logcounts

Issue - State: closed - Opened by Nayrouz109 about 2 years ago - 4 comments

#109 - Mixed model approach with paired sample design

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

#108 - error with pbDS: how to set the correct parameters

Issue - State: closed - Opened by yamihn over 2 years ago - 1 comment

#107 - Passing filter parameters to pbDS

Pull Request - State: open - Opened by dbdimitrov over 2 years ago - 1 comment

#106 - Updated citation to journal publication

Pull Request - State: closed - Opened by molecules over 2 years ago - 1 comment

#105 - Error in .check_args_pbHeatmap

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

#104 - Possible bug in simData function

Issue - State: open - Opened by simonemodolo over 2 years ago

#103 - Analysing DEG in Spatial visium data

Issue - State: open - Opened by vkjain0006 over 2 years ago - 2 comments

#102 - possible bug in resDS for some methods

Issue - State: open - Opened by AnjaliC4 over 2 years ago

#100 - quick question about filtering of genes

Issue - State: closed - Opened by AnjaliC4 over 2 years ago - 1 comment

#99 - How to set up interactions?

Issue - State: closed - Opened by AnjaliC4 over 2 years ago - 1 comment

#98 - error in vst sctransform

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

#97 - cannot compute log geometric means Deseq2

Issue - State: open - Opened by AnjaliC4 over 2 years ago - 2 comments

#96 - p_adj.loc greater than p_adj.glb

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

#94 - full list of genes

Issue - State: closed - Opened by AnaBVA over 2 years ago - 1 comment

#93 - pbHeatmap error because 't' is not implemented for 'Matrix'

Issue - State: open - Opened by AnaBVA over 2 years ago - 3 comments

#92 - Muscat compared to Distinct

Issue - State: closed - Opened by chris-rands almost 3 years ago - 1 comment

#91 - Example code from prepSCE does not work with aggregateData

Issue - State: closed - Opened by dariober almost 3 years ago - 1 comment

#90 - muscat with no replicates?

Issue - State: closed - Opened by nuriabonetm almost 3 years ago - 1 comment

#88 - Importing seurat object directly to muscat

Issue - State: closed - Opened by ps120195 almost 3 years ago - 5 comments

#87 - weighting the samples according to the number of cells

Issue - State: open - Opened by stkachev almost 3 years ago

#86 - Potential bug in the prepSim code

Issue - State: closed - Opened by wanghao98 almost 3 years ago - 1 comment

#85 - pbHeatmap doesn't match DS gene list?

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

#84 - Error when simulating data use my own sce object

Issue - State: closed - Opened by wanghao98 about 3 years ago - 10 comments

#83 - Is the counts and logcounts in aggregateData from SCT

Issue - State: closed - Opened by bassanio about 3 years ago - 2 comments

#82 - Setting FORCE in simData to increase the number of samples

Issue - State: closed - Opened by SirKuikka about 3 years ago - 1 comment

#81 - prepSim error

Issue - State: closed - Opened by YingxinLin about 3 years ago - 1 comment

#80 - dummy 'kid' variable for whole dataset DE

Issue - State: closed - Opened by lindsaynhayes about 3 years ago - 1 comment

#79 - error in dataset simulation: length(class) == 1L is not TRUE

Issue - State: open - Opened by YiyiChen0328 over 3 years ago - 2 comments

#78 - Error in x[[1]] : subscript out of bounds when running pbDS()

Issue - State: closed - Opened by Yale73 over 3 years ago - 18 comments

#77 - aggregateData Output: How to fetch and write for individual assay

Issue - State: closed - Opened by bassanio over 3 years ago - 1 comment

#76 - Error in aggregate Output

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

#75 - Trouble loading data from GSE96583

Issue - State: closed - Opened by meghamsh738 over 3 years ago - 1 comment

#74 - Cell-level analysis: Vst method

Issue - State: open - Opened by bassanio over 3 years ago - 4 comments

#73 - Seurat object for DE : Error metadata(pbs)$experiment_info) is not TRUE

Issue - State: closed - Opened by bassanio over 3 years ago - 1 comment

#72 - The p_adj.loc results

Issue - State: open - Opened by yuyingxie over 3 years ago - 2 comments

#71 - How to speed up 'binom'

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

#70 - How to set BPPARAM to run parallel

Issue - State: open - Opened by lindsaynhayes over 3 years ago - 4 comments

#69 - Different global and local p value for testing only 1 cluster

Issue - State: closed - Opened by wanghao98 over 3 years ago - 3 comments

#68 - Muscat doesn't work with one cluster anymore

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

#67 - Missing dependency: statmod

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

#66 - What is the meaning of the "scale" parameter of the "aggregateData" function?

Issue - State: closed - Opened by altairwei over 3 years ago - 4 comments
Labels: documentation

#65 - Problem using covariates with mmDS

Issue - State: open - Opened by lvclark over 3 years ago - 2 comments

#64 - Add rowData to pb object

Issue - State: closed - Opened by wmacnair over 3 years ago

#63 - library size correction

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

#63 - library size correction

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

#62 - pbDS() makes error: identical(assayNames(pbs), rownames(n_cells)) is not TRUE

Issue - State: closed - Opened by dmsalsgh97 over 3 years ago - 6 comments

#61 - `prepSCE`: only replace colData of original SCE

Pull Request - State: closed - Opened by milanmlft over 3 years ago

#60 - Proposal: rename the example `sce` dataset

Issue - State: closed - Opened by milanmlft over 3 years ago - 1 comment

#60 - Proposal: rename the example `sce` dataset

Issue - State: closed - Opened by milanmlft over 3 years ago - 1 comment

#58 - nbinom1 vs nbinom2 parameterisation

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

#57 - pbDS normalization

Issue - State: closed - Opened by lucia-ramirez almost 4 years ago

#56 - unexpected results: mixed models for B cells

Issue - State: open - Opened by victorkleb almost 4 years ago - 5 comments

#55 - How to set coef for mmDS

Issue - State: open - Opened by yuyingxie almost 4 years ago - 5 comments

#54 - Tests for three groups

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

#53 - The DESeq2 Method for DS Analysis through muscat

Issue - State: open - Opened by ms11863 almost 4 years ago - 1 comment

#52 - Error when colnames(assays(sce)) != rownames(colData(sce))

Issue - State: open - Opened by frenkiboy almost 4 years ago

#50 - Add vignette section demonstrating pbDS for complex models

Issue - State: open - Opened by wmacnair almost 4 years ago - 2 comments

#49 - Move n_cells from metadata to int_colData

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

#48 - Speed up aggregateData()

Issue - State: closed - Opened by HelenaLC almost 4 years ago - 2 comments
Labels: enhancement

#47 - Parallelisation of pbDS()

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

#46 - How to analyze Seurat subcluster data through Muscat

Issue - State: closed - Opened by priyamnarain about 4 years ago

#45 - mmDS using 'nbinom'

Issue - State: closed - Opened by yuyingxie about 4 years ago - 4 comments

#44 - Warning for running mmDS

Issue - State: open - Opened by yuyingxie about 4 years ago - 6 comments

#43 - Add control for direction of type genes

Pull Request - State: open - Opened by ansonrel about 4 years ago

#42 - pbDS takes very long time

Issue - State: closed - Opened by crazyhottommy about 4 years ago - 1 comment