RGLab/MAST

Issues

• Can NOT install MAST

  #189 opened 4 months ago by nhu-github
  0

• DEG counts are associated with the number of cells

  #188 opened 4 months ago by ZunpengLiu
  0

• Error: grouping factors must have > 1 sampled level

  #187 opened 6 months ago by andrewsong777
  0

• Error in getClassDef(x@superClass, package = packageSlot(x))@virtual : no applicable method for `@` applied to an object of class "NULL"

  #184 opened 8 months ago by nfancy
  10

• Got error when using summary(zlmCond.glmer)

  #186 opened 7 months ago by fnhe
  1

• Segfaults

  #185 opened 7 months ago by mspivakov
  3

• getLogFC cannot accept hypothesis as contrast0 due to internal transpose

  #181 opened a year ago by derrik-gratz
  0

• Error in validObject(.Object): invalid class “corMatrix” object: 'sd' slot has nonfinite elements

  #180 opened a year ago by derrik-gratz
  7

• MAST uses all cores even after setting mc.cores

  #152 opened 3 years ago by fbnrst
  5

• "R CMD check" failure on Linux ARM64

  #179 opened a year ago by martin-g
  6

• lrTest's with CoefficientHypothesis and contrast matrix give inconsistent results

  #178 opened a year ago by ImNotaGit
  0

• bug: MAST returns error after Seurat SCTransform, v2 regularization

  #175 opened a year ago by grhogg
  10

• p values not reported for all features

  #177 opened 2 years ago by susheelbhanu
  0

• FindAllMarkers issue

  #176 opened 2 years ago by andrew2k
  1

• Convergence issues due to all cells in comparison expressed certain genes?

  #151 opened 4 years ago by hoholee
  2

• Error: invalid name for slot of class “BayesGLMlike”: logfc.tLReshold

  #174 opened 2 years ago by avpatel18
  2

• Low logFCs and failure to converge?

  #173 opened 2 years ago by learning-MD
  0

• MAST v.1.21.3 -- Error: $ operator is invalid for atomic vectors

  #170 opened 3 years ago by akhst7
  7

• Support for passing hypothesis to doLRT in summary() as in lrTest()

  #171 opened 3 years ago by ImNotaGit
  6

• LFC interpretation

  #167 opened 3 years ago by rajewski
  1

• How to calculate logFC for condition in a mixed effects model with MAST?

  #147 opened 3 years ago by esrasefik
  15

• Restricted Maximum Likelihood or Maximum Likelihood for estimating parameters in mixed effect model using MAST?

  #157 opened 3 years ago by sofiapuvogelvittini
  3

• What are the meanings of the components "CDHS" in the "zlm" function?

  #162 opened 3 years ago by danli349
  3

• Parallelization for summary() with doLRT; Passing a design matrix to zlm()

  #169 opened 3 years ago by ImNotaGit
  1

• What should I do with the "NaN" values, with extremely small `Pr(>Chisq)` in the `coef` column of the `summary(zlmCond)` result?

  #168 opened 3 years ago by danli349
  0

• gseaAfterBoot enriched genes

  #154 opened 3 years ago by EBosi
  5

• Applicability of MAST to spatial transcriptomics analyses without single-cell resolution

  #166 opened 3 years ago by jeremycfd
  0

• When I run `zlm` with several clusters, how to compare 1 cluster versus all the others?

  #165 opened 3 years ago by danli349
  1

• time course DE analysis

  #164 opened 3 years ago by shokohirosue
  1

• Multiple variables, single coefficient

  #163 opened 3 years ago by kanefos
  2

• Comparisons among three conditions

  #161 opened 3 years ago by sofiapuvogel
  1

• p value = 0

  #160 opened 3 years ago by shokohirosue
  2

• GSEA background sets of genes

  #159 opened 3 years ago by sofiapuvogel
  2

• Selecting count data in zlm function

  #158 opened 3 years ago by IrSoler
  9

• Segmentation fault

  #156 opened 3 years ago by Santos22903
  1

• Deviance

  #155 opened 3 years ago by sofiapuvogelvittini
  2

• Understanding zlm with Batch effects for Differential Expression Analysis

  #153 opened 3 years ago by jtlandis
  1

• Update README.md to reflect removal of 'MAST-intro' vignette

  #150 opened 4 years ago by compbiolover
  0

• Changes to Matrix::rankMatrix break tests

  #149 opened 4 years ago by amcdavid
  2

• Problems when fitting a linear-mixed model ('glmer') with sc-RNAseq data

  #148 opened 4 years ago by aidarripoll
  4

• Error in zlm

  #145 opened 4 years ago by Samantha-Czn
  7

• Error: grouping factors must have > 1 sampled level

  #146 opened 4 years ago by esrasefik
  4

• Resource requirements for large sparse matrices

  #138 opened 4 years ago by combiz
  6

• DE between different groups : post-hoc tests?

  #139 opened 4 years ago by fabien-tell
  3

• Unexpected Large Confidence Interval of LogFC

  #142 opened 4 years ago by JiaxinLi-lipluszn
  2

• Discrepancy between including factors as covariates directly vs hard-coding dummy variables

  #144 opened 4 years ago by jmchan88
  5

• warning messages: In rbind(...) : number of columns of result is not a multiple of vector length

  #143 opened 4 years ago by wangjingshen
  9

• Unable to calculate log-ratio test for interaction term

  #141 opened 4 years ago by jmchan88
  5

• Units of logFC for a numeric dependent variable

  #140 opened 4 years ago by combiz
  5

• P-value vs. log fold change discrepancies when fitting a model with a covariate

  #137 opened 4 years ago by argschwind
  2