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Seurat v4.0.1#4247

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mojaveazure merged 119 commits intomastersatijalab/seurat:masterfrom developsatijalab/seurat:developCopy head branch name to clipboardMar 18, 2021

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Commits on Feb 1, 2021

• Update visualization.R

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Commits on Feb 5, 2021

• better cell naming consistency in Read10X

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• update NEWS, bump version

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• Merge pull request #520 from satijalab/fix/Read10X_names

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• Add documentation

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• Merge remote-tracking branch 'upstream/develop' into patch-1

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• bump version; update NEWS

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• Merge pull request #4005 from hoondy/patch-1

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Commits on Feb 6, 2021

• Track feature1 parameters in feature.attributes of SCTAssay

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Commits on Feb 8, 2021

• Merge branch 'master' into develop

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Commits on Feb 9, 2021

• Merge branch 'develop' into feat/sctassay_step1

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• bump version

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• Add concept

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• Merge pull request #522 from satijalab/feat/sctassay_step1

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• Add spatial concept

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• Fix anchor filtration

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• Merge branch 'develop' into fix/annotateanchors

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• Update release notes"

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Commits on Feb 10, 2021

• Merge branch 'develop' into doc/annotateanchors

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• Merge pull request #524 from satijalab/fix/annotateanchors

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• Merge branch 'develop' into doc/annotateanchors

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• Merge pull request #523 from satijalab/doc/annotateanchors

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Commits on Feb 12, 2021

• HVFInfo for SCTAssay

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• fix bug for all variable genes

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• Add documentation

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• Bump develop version

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Commits on Feb 13, 2021

• Merge pull request #525 from satijalab/feat/HVFInfo_SCTAssay

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• change negihbor default name

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• update tests neighbor name

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Commits on Feb 18, 2021

• Modify Read10X for GEO compatibility

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• Merge branch 'master' into develop

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Commits on Feb 19, 2021

• fix pseudocount in FindMarkers.Assay

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• fix mean.fxn and fc.name in FindMarkers.DimReduc

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• Update reference.reduction documentation

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• pass assay param properly

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• Merge pull request #529 from satijalab/docs/refreduc

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Commits on Feb 22, 2021

• Merge pull request #4111 from lldelisle/fixPseudoCount

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• Merge branch 'develop' of github.com:satijalab/seurat into develop

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• Increase dev version

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• Merge branch 'develop' of github.com:satijalab/seurat-private into develop

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• Merge branch 'develop' into fix/RunLDA

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• Merge pull request #533 from satijalab/doc/releasenotes

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• Merge branch 'develop' into fix/RunLDA

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• bump version, update NEWS

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• Merge pull request #530 from satijalab/fix/RunLDA

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Commits on Feb 25, 2021

• redev

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• redev2

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• Add cols param JackStrawPlot

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• fix manual entry

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• Changed order=T behavior in SingleDimPlot - Order first by NAs and only then by value - causes NA cells to be printed first

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• Merge branch 'master' into develop

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Commits on Feb 26, 2021

• check nn.name input type

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• format update

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• Merge branch 'develop' into feat/neighbors_name

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• bump version

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• change return neighbor message

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• Merge pull request #526 from satijalab/feat/neighbors_name

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• Merge branch 'develop' into feat/check_nn.name

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• check neighbors and graph

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• Update documentation for FindNeighbors; #4155

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• Merge branch 'develop' of github.com:satijalab/seurat into develop

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• Merge branch 'develop' into JackStrawPlot_Color

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• run docs

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• bump version, update NEWS

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Commits on Feb 27, 2021

• Merge pull request #4149 from samuel-marsh/JackStrawPlot_Color

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• Merge branch 'develop' into nas_first_plots

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• bump version, update NEWS

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• Merge pull request #4153 from GreenGilad/nas_first_plots

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• Add ReadMtx() to read local and remote mtx files

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• Update doc

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• Shorten doc example

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• Fix local file support

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Commits on Mar 1, 2021

• Merge branch 'develop' into doc/find_neighbors

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• Merge branch 'develop' into feat/check_nn.name

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• Minor style fixes

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• Bump develop version

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Commits on Mar 3, 2021

• Merge pull request #537 from satijalab/doc/find_neighbors

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Commits on Mar 4, 2021

• Reduce code duplication

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• Fixes for Online

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• Fixes for Online

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• Merge branch 'develop' into feat/check_nn.name

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• Bump develop version

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• Fix variable name for data

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• Update NEWS

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• Fix swapped feature/cell, add text=T for gzcon

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Commits on Mar 5, 2021

• use equality thresholds in FindMarkers

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• Increase min.pct in test

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• Remove on.exit as connections autoclose

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• Merge branch 'develop' into feat/ReadMtx

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Commits on Mar 6, 2021

• Clean up

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• Merge branch 'feat/ReadMtx' of github.com:satijalab/seurat-private into feat/ReadMtx

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• Add tests

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• Swap test

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• Fix test

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Commits on Mar 12, 2021

• Dont specify

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• Update NEWS.md

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• bump version

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• Merge pull request #539 from satijalab/fix/diffexp.thresholds

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• Merge remote-tracking branch 'upstream/develop'

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Commits on Mar 15, 2021

• fix imports with spatstat update

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• bump version, update NEWS

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• Merge pull request #4216 from Alanocallaghan/master

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• Merge branch 'develop' into fix/spatstat

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• bump version, update NEWS

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• Merge pull request #540 from satijalab/fix/spatstat

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• merge

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• Merge pull request #535 from satijalab/feat/check_nn.name

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• Merge branch 'develop' into feat/ReadMtx

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• Style fixes

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• devtools::document updated this

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• Minor fixes

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• Attempt to trigger GH Actions

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Commits on Mar 16, 2021

• bump version, update NEWS

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• skip ReadMtx tests on CRAN

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• Merge pull request #538 from satijalab/feat/ReadMtx

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Commits on Mar 17, 2021

• Prep release 4.0.1

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• Fix line length in documentation

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• Update link to Travis CI

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• Merge pull request #541 from satijalab/release/4.0.1

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