statOmics/tradeSeq

Issues

• earlyDEtest interpretation

  #267 opened 3 months ago by ishars00
  1

• AIC charts give incorrect relative AIC value

  #262 opened 5 months ago by beazors
  1

• Problem with coloring dots using pointCol in plotSmoothers

  #266 opened 3 months ago by beazors
  1

• BPPARAM with fitGAM

  #258 opened 9 months ago by AndreaYCT
  8

• Combining multiple gams together

  #265 opened 3 months ago by rayajallad
  0

• Interpreting earlyDE test when # of knots is not equal among lineages

  #264 opened 4 months ago by beazors
  2

• Extracting middle knot dots when using embedCurves from slingshot

  #263 opened 5 months ago by kmh005
  0

• Discrepancy between `plotSmoothers` and `predictSmooth`

  #232 opened 2 years ago by nickhir
  5

• Error in .local(counts, ...) : Either provide the slingshot object using the sds argument, or provide pseudotime and cell-level weights manually using pseudotime and cellWeights arguments.

  #254 opened 7 months ago by chungsai
  1

• figGAM is not adhering to BPPARAM limits.

  #259 opened 8 months ago by dfermin
  1

• Using BatchtoolsParam() in fitGAM()

  #261 opened 6 months ago by Alexis-Varin
  0

• Error: impossible to place a knot at all endpoints

  #246 opened 7 months ago by crist156
  4

• Association of gene expression with pseudotime

  #249 opened a year ago by A-legac45
  10

• predictSmooth is calculating super high values for lowly expressed genes

  #252 opened a year ago by yashuap
  5

• plotSmoothers curves seem to contradict startVsEndTest logFC

  #255 opened 7 months ago by Dazcam
  6

• Dealing with multiple root nodes

  #253 opened 7 months ago by Dazcam
  1

• Poor distribution of cluster sizes

  #251 opened 7 months ago by yashuap
  4

• Pitfalls of testing between conditions (ConditionTest())

  #250 opened 7 months ago by Jaimelan
  5

• Monocle3 as input to tradeSeq

  #247 opened a year ago by jiangzh-coder
  3

• DEG from tradeseq

  #260 opened 7 months ago by synatkeamsk
  1

• Identifying knots on multi-curve plot

  #226 opened 2 years ago by fluentin44
  5

• How to compare Seurat Log2FC with TradeSeq Log2FC

  #256 opened 10 months ago by No2Ross
  0

• problem output assoress lineage = TRUE which column correspond to what

  #248 opened 10 months ago by A-legac45
  3

• Finds and orders `reduced` gene expressoin along a lineage

  #243 opened a year ago by pchiang5
  4

• Reducing dataset size to improve run time

  #223 opened 2 years ago by fluentin44
  4

• plotsmoothers

  #233 opened a year ago by nouhay
  1

• evaluateK

  #238 opened a year ago by zhangol
  1

• evaluatek never completes

  #240 opened a year ago by eblchen
  1

• Saving memory by splitting the object?

  #245 opened a year ago by jjia1
  0

• choosing knot

  #244 opened a year ago by AndreaYCT
  2

• Add an extra column in the output of conditionTest() with log2fc results

  #234 opened 2 years ago by gabrielnegreira
  3

• query about conditionTest significant genes

  #237 opened 2 years ago by EH0234
  6

• running fitGAM on Single cell expt object for multiple lineages

  #242 opened a year ago by klai001
  1

• Add curves Labels to plotGeneCount

  #222 opened a year ago by Sidy2015
  3

• Question about lineage assignment

  #217 opened a year ago by KemperNiklas
  2

• Is it possible to balance the sequencing depth between multiple libraries?

  #231 opened a year ago by Siteng999
  2

• startVsEndTest yields results for non existing pseudotimeValues

  #239 opened a year ago by sam-israel
  1

• memory shortage after finalizing the model fitting

  #225 opened 2 years ago by Abeer-hes
  6

• Plotting own trajectories to use with tradeSeq [Question]

  #236 opened 2 years ago by Tommy0398
  1

• access to the line in plotsmoothers

  #235 opened 2 years ago by nouhaylaeraysy
  0

• Differential expression between conditions between separate slingshot objects

  #228 opened 2 years ago by nickhir
  2

• associationTest for multiple conditions

  #227 opened 2 years ago by flde
  2

• predictSmooth vs plotSmoothers

  #230 opened 2 years ago by flde
  2

• about the relative levels between 2 lineages of interest

  #229 opened 2 years ago by pchiang5
  1

• Remove spurious rowData calls in hypothesis tests.

  #216 opened 2 years ago by jgilis
  1

• associationTest is renaming Lineages instead of reusing them

  #224 opened 2 years ago by ccasar
  0

• Running time for fitGAM

  #220 opened 2 years ago by Sa753
  3

• Adapting to cytometry data?

  #221 opened 2 years ago by 83years
  1

• Question of cutomized trajectory and pseudotime calculation

  #218 opened 2 years ago by lengfei5
  1

• Enquiry on downsampling to ensure balance of conditions along pseudotime for conditionTest

  #219 opened 2 years ago by JesseRop
  2