Commits

Branch selector

 master

User selector

ChristophH

Datepicker

All time

Commit History

Commits on Apr 10, 2019

• Temp fix for setting of feature meta data in SCTransform

remove the @meta.features once automatic NA padding is part of [[<- for assay objects

  ChristophH

  committed
  d419e71

  Copy full SHA for d419e71

• Merge branch 'release/3.0' of https://github.com/satijalab/seurat-private into release/3.0

  ChristophH

  committed
  6c02ab0

  Copy full SHA for 6c02ab0

• Make VariableFeaturePlot work with SCTransform workflow

  ChristophH

  committed
  9752109

  Copy full SHA for 9752109

Commits on Apr 9, 2019

• Update SCTransform wrapper

  ChristophH

  committed
  23a4b5b

  Copy full SHA for 23a4b5b

• Add conserve.memory parameter to SCTransform; if TRUE we will never hold a full residual matrix in memory (only for variable features)

  ChristophH

  committed
  517c83b

  Copy full SHA for 517c83b

• devtools::document() changed this

  ChristophH

  committed
  31ba362

  Copy full SHA for 31ba362

• Set return.only.var.genes to TRUE in SCTransform

  ChristophH

  committed
  c537a9a

  Copy full SHA for c537a9a

• Overhaul SCTransform to allow for three-step processing of data by sctransform package

If only variable genes are to be returned, the normalization is broken up into three steps: 1) get regularize…

  Show description for 528a89d
  ChristophH

  committed
  528a89d

  Copy full SHA for 528a89d

• Make SCTransform always return gene attributes

  ChristophH

  committed
  5e473d3

  Copy full SHA for 5e473d3

• Merge branch 'release/3.0' of https://github.com/satijalab/seurat into release/3.0

  ChristophH

  committed
  a89daa6

  Copy full SHA for a89daa6

Commits on Apr 8, 2019

• Cleaning up SCTransform

  ChristophH

  committed
  4fe5258

  Copy full SHA for 4fe5258

Commits on Apr 4, 2019

• Fix message regarding new assay name in SCTransform

  ChristophH

  committed
  09ca700

  Copy full SHA for 09ca700

Commits on Apr 3, 2019

• Make new assay name a parameter in SCTransform

  ChristophH

  committed
  e2c1a0c

  Copy full SHA for e2c1a0c

• Add detail to message in ScaleData.default

  ChristophH

  committed
  e9b48a3

  Copy full SHA for e9b48a3

Commits on Apr 2, 2019

• Pass verbose to ScoreAnchors

  Show description for 43e616a
  ChristophH

  committed
  43e616a

  Copy full SHA for 43e616a

• Fix typo in DietSeurat; add error message if data = FALSE

  Show description for 46de004
  ChristophH

  committed
  46de004

  Copy full SHA for 46de004

Commits on Mar 20, 2019

• Make sure SCTransform does not try to return more features than are present in the input assay

  ChristophH

  committed
  87ff635

  Copy full SHA for 87ff635

• devtools::document() changed this

  ChristophH

  committed
  2200e5d

  Copy full SHA for 2200e5d

• Add a set.seed parameter to SCTransform; default is 1448145.

  ChristophH

  committed
  4fb59d3

  Copy full SHA for 4fb59d3

• Make block size passed to ScaleData sufficiently small in SCTransform

  Show description for 4cfbd77
  ChristophH

  committed
  4cfbd77

  Copy full SHA for 4cfbd77

Commits on Mar 18, 2019

• Replace hard coded block size of 200 with parameter (default 1000) for RegressOutMatrix in ScaleData.default

  ChristophH

  committed
  c172d9e

  Copy full SHA for c172d9e

Commits on Mar 12, 2019

• Change default SCTransform parameters: 3000 variable genes; return only variable genes; clip residuals to sqrt(n/30)

  ChristophH

  committed
  a6254ee

  Copy full SHA for a6254ee

• Bugfix: Subset latent.data before passing to ScaleData.default since that function uses all columns by default

  ChristophH

  committed
  42abe75

  Copy full SHA for 42abe75

• Fix bug where vars.to.regress was never passed to ScaleData in SCTransform

  ChristophH

  committed
  405393c

  Copy full SHA for 405393c

• Set default assay to use in SCTransform to RNA; used to be set to NULL (default assay) but this lead to problems when SCTransform is called multiple times

  ChristophH

  committed
  01ad8e7

  Copy full SHA for 01ad8e7

Commits on Mar 11, 2019

• Add vars.to.regress parameter to SCTransform; pass to ScaleData

  ChristophH

  committed
  06ff296

  Copy full SHA for 06ff296

• Wrap Parenting in ScaleData.default in tryCatch

  ChristophH

  committed
  deb3081

  Copy full SHA for deb3081

Commits on Mar 5, 2019

• Clip residuals before any centering or scaling is done in SCTransform

  ChristophH

  committed
  0eed3bf

  Copy full SHA for 0eed3bf

• Check if there is more than one type before printing message in Read10X

  ChristophH

  committed
  2cc42f5

  Copy full SHA for 2cc42f5

• Add option to SCTransform to subset results to only variable genes

  ChristophH

  committed
  25a90e6

  Copy full SHA for 25a90e6

Commits on Mar 4, 2019

• Rename SCTransform output assay to SCT

  ChristophH

  committed
  75f134f

  Copy full SHA for 75f134f

• Renamed RegressRegNB to SCTransform

  ChristophH

  committed
  e34a621

  Copy full SHA for e34a621

• In REgressRegNB create new assay for results instead of overwriting input assay; by default output counts will be corrected counts, data will be log1p(counts), and scale.data will be pearson residuals

  ChristophH

  committed
  c8048fe

  Copy full SHA for c8048fe

• devtools::document() changed this

  ChristophH

  committed
  a714f67

  Copy full SHA for a714f67

• In RegressRegNB use 2000 variable genes by default

  ChristophH

  committed
  aad64bf

  Copy full SHA for aad64bf

Pagination

Previous

Next