mojaveazure/seurat-object issues and pull requests

#172 - Recent changes to Matrix break installed SeuratObject

Issue - State: closed - Opened by hpages 8 months ago - 4 comments

#171 - Two fixes to no longer use deprecated routines

Pull Request - State: closed - Opened by mojaveazure 8 months ago

#170 - Release/5.0.1

Pull Request - State: open - Opened by mojaveazure 8 months ago

#169 - Adjust relocation of on-disk layers

Pull Request - State: closed - Opened by mojaveazure 8 months ago

#168 - Assay5 cannot use pattern argument in the PercentageFeatureSet() function

Issue - State: closed - Opened by jackaloppy 8 months ago

#167 - readRDS(object) requires UpdateSeuratObject(object) - results in Error in [[<-: ! Cannot add new cells with [[<-

Issue - State: open - Opened by MGjorgoska 8 months ago - 3 comments

#166 - Matrix 1.6.2 issue? invalid class "Graph" object: superclass "mMatrix" not defined in the environment of the object's class

Issue - State: closed - Opened by bbimber 8 months ago - 7 comments

#165 - .GetSeuratCompat error while using SCTransform with v2 regularization

Issue - State: closed - Opened by ishwarvh 8 months ago

#164 - Bump Matrix version

Pull Request - State: closed - Opened by mojaveazure 8 months ago

#163 - Update class imports from Matrix

Pull Request - State: closed - Opened by mojaveazure 8 months ago

#162 - LogMap error in R-devel with Matrix 1.6-2

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

#161 - Create Seurat Object from matrix and two text files

Issue - State: open - Opened by sky5198 8 months ago

#160 - Update use of `GetAssayData()`

Pull Request - State: closed - Opened by mojaveazure 8 months ago

#159 - Release 5.0.0

Pull Request - State: closed - Opened by mojaveazure 9 months ago

#158 - Move SeuratObject v5 to `develop`

Pull Request - State: closed - Opened by mojaveazure 9 months ago

#157 - AddMetaData with data.frame as `metadata` fills NAs instead of data

Issue - State: open - Opened by jonasfreimuth 9 months ago

#156 - Remove restrictions on which layers get merged in v5 assays

Pull Request - State: closed - Opened by mojaveazure 9 months ago

#155 - Add compatibility mode for Seurat v4

Pull Request - State: closed - Opened by mojaveazure 9 months ago

#154 - Add BPCells support for `SaveSeuratRds()` and `LoadSeuratRds()`

Pull Request - State: closed - Opened by mojaveazure 9 months ago

#153 - Fix LogMap subsetting not preserving object order

Pull Request - State: closed - Opened by mojaveazure 9 months ago

#152 - Crop not working due to sp over() deprecation

Pull Request - State: closed - Opened by zskylarli 9 months ago

#151 - Update bracket behavior for assays

Pull Request - State: closed - Opened by mojaveazure 9 months ago

#150 - BPCells issue in FindTransferAnchors + adist()

Pull Request - State: closed - Opened by Gesmira 9 months ago

#149 - Seurat5 VariableFeatures, Layer defaults, split, whichcells

Pull Request - State: closed - Opened by Gesmira 9 months ago

#148 - Merge v4 into v5 devel

Pull Request - State: closed - Opened by mojaveazure 9 months ago

#147 - VariableFeatures updates

Pull Request - State: closed - Opened by Gesmira 9 months ago

#146 - Provide unified deprecation function

Pull Request - State: closed - Opened by mojaveazure 9 months ago

#145 - Please specify Matrix version with equal separation signs

Issue - State: closed - Opened by tillea 9 months ago - 5 comments

#144 - Gm setlayerdefaults

Pull Request - State: closed - Opened by Gesmira 9 months ago

#143 - Gm var features

Pull Request - State: closed - Opened by Gesmira 9 months ago

#142 - split warnings

Pull Request - State: closed - Opened by Gesmira 9 months ago

#141 - Which cells fix (new)

Pull Request - State: closed - Opened by longmanz 9 months ago - 1 comment

#140 - updated split warning

Pull Request - State: closed - Opened by Gesmira 9 months ago

#139 - added_whichCells

Pull Request - State: closed - Opened by longmanz 9 months ago

#138 - forcing dgcmatrix if not specific type

Pull Request - State: closed - Opened by Gesmira 9 months ago

#137 - Error in parse(outFile)

Issue - State: open - Opened by yanwuanxin 9 months ago - 2 comments

#136 - Forcing coercion to dgCMatrix if not "dgCMatrix, IterableMatrix, or DelayedArray

Pull Request - State: closed - Opened by Gesmira 9 months ago

#135 - improve WhichCells

Pull Request - State: closed - Opened by longmanz 9 months ago - 1 comment

#134 - Draft: Split.StdAssay

Pull Request - State: closed - Opened by Gesmira 9 months ago

#133 - Draft: SetLayerDefaults

Pull Request - State: closed - Opened by Gesmira 9 months ago

#132 - Draft: Fixing v5 VariableFeatures

Pull Request - State: closed - Opened by Gesmira 9 months ago

#131 - Split.StdAssay

Pull Request - State: closed - Opened by Gesmira 9 months ago

#130 - no slot of name "images" for this object of class "Seurat"

Issue - State: open - Opened by jzhou54 9 months ago - 2 comments

#129 - subset.Seurat: Making downsample specific to default assay

Pull Request - State: open - Opened by Gesmira 9 months ago

#128 - Fixing v5 VariableFeatures

Pull Request - State: closed - Opened by Gesmira 10 months ago

#127 - Weird issue with doing operations when ncells = nfeatures

Issue - State: open - Opened by saketkc 10 months ago

#126 - Stop auto transposition in `.PrepLayerData2()`

Pull Request - State: closed - Opened by mojaveazure 10 months ago

#125 - Adding feature metadata to Seurat v5 Object using SeuratObject::AddMetaData does not work

Issue - State: open - Opened by grantn5 10 months ago

#124 - Setting Layer Defaults

Pull Request - State: closed - Opened by Gesmira 10 months ago

#123 - Release 4.1.4

Pull Request - State: closed - Opened by mojaveazure 10 months ago

#122 - Add check for newer ABIs

Pull Request - State: closed - Opened by mojaveazure 10 months ago

#121 - Add `.BPMatrixMode`

Pull Request - State: closed - Opened by mojaveazure 10 months ago

#120 - Warnings and BPCells exported function

Pull Request - State: closed - Opened by Gesmira 10 months ago

#119 - change AddMetaData method for assay, allows people to add feature lev…

Pull Request - State: closed - Opened by mhkowalski 10 months ago

#118 - Remove `rgeos` from suggests and add `sf`

Pull Request - State: closed - Opened by AustinHartman 12 months ago

#117 - add error message if images slot is not present (old seurat objects)

Pull Request - State: closed - Opened by mhkowalski 12 months ago

#116 - Add checks for layer number and feature presence in `LayerData()`/`GetAssayData()`

Pull Request - State: closed - Opened by yuhanH about 1 year ago - 1 comment

#115 - Feat/layer names

Pull Request - State: open - Opened by mhkowalski about 1 year ago

#114 - Update feature-level AddMetaData

Pull Request - State: open - Opened by AustinHartman about 1 year ago

#113 - Seurat5 devel

Pull Request - State: closed - Opened by yuhanH about 1 year ago

#112 - Feat/double bracket error msg

Pull Request - State: closed - Opened by mhkowalski about 1 year ago

#111 - modify fetch data layer

Pull Request - State: closed - Opened by yuhanH about 1 year ago - 1 comment

#110 - merge()

Pull Request - State: closed - Opened by Gesmira about 1 year ago

#109 - sf in DESCRIPTION suggets due to legacy packahe rgeos

Issue - State: closed - Opened by ricrossi about 1 year ago - 4 comments

#108 - Merge runs forever without error if `x` is inside a named vector

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

#107 - remove R>=4.1.0 anonymous function shorthand

Pull Request - State: closed - Opened by AustinHartman about 1 year ago

#106 - Modifying saveRDS for BPCells + other v5 updates

Pull Request - State: closed - Opened by Gesmira about 1 year ago

#105 - Seurat5

Pull Request - State: open - Opened by yuhanH about 1 year ago

#104 - Allow for filtering of BPCells matrices in CreateSeuratObject

Pull Request - State: closed - Opened by Gesmira over 1 year ago

#103 - Feat/cal n generic

Pull Request - State: closed - Opened by yuhanH over 1 year ago

#102 - fix check layer name

Pull Request - State: closed - Opened by yuhanH over 1 year ago

#101 - Feat/cal n generic

Pull Request - State: closed - Opened by yuhanH over 1 year ago

#100 - Feat/v5assay create

Pull Request - State: closed - Opened by yuhanH over 1 year ago

#99 - Feat/cal n generic

Pull Request - State: closed - Opened by yuhanH over 1 year ago

#98 - Feat/cal n generic

Pull Request - State: closed - Opened by yuhanH over 1 year ago

#97 - Feat/cal n generic

Pull Request - State: closed - Opened by yuhanH over 1 year ago

#96 - naming layers

Pull Request - State: closed - Opened by Gesmira over 1 year ago - 3 comments

#95 - Feat/cal n generic

Pull Request - State: closed - Opened by yuhanH over 1 year ago

#94 - Feat/cal n generic

Pull Request - State: closed - Opened by yuhanH over 1 year ago

#93 - Feat/cal n generic

Pull Request - State: closed - Opened by yuhanH over 1 year ago

#92 - Use newer version of Matrix

Pull Request - State: closed - Opened by mojaveazure over 1 year ago

#91 - Saving BPCells directories and .rds file in same directory

Pull Request - State: closed - Opened by Gesmira over 1 year ago - 1 comment

#90 - how to provide X-Y coordinates for spatial assay using CreateSeuratObject

Issue - State: closed - Opened by linpei26 over 1 year ago - 3 comments

#89 - Fix missing median_umi slot in SCT assay

Pull Request - State: closed - Opened by saketkc over 1 year ago

#88 - v5 --> v3 assays

Pull Request - State: closed - Opened by Gesmira over 1 year ago

#87 - naming of parameters in RenameAssays

Pull Request - State: closed - Opened by Gesmira over 1 year ago

#86 - fix layer in VariableFeatures

Pull Request - State: closed - Opened by yuhanH over 1 year ago

#85 - new proposed way of dealing with variables and strings for assay name

Pull Request - State: closed - Opened by Gesmira over 1 year ago

#84 - allowing both variable names and assay name as input

Pull Request - State: closed - Opened by Gesmira over 1 year ago

#83 - Update key name during merge

Pull Request - State: closed - Opened by AustinHartman over 1 year ago

#82 - Feat/assay v5

Pull Request - State: closed - Opened by Gesmira over 1 year ago

#81 - fix no cells in assay

Pull Request - State: closed - Opened by yuhanH over 1 year ago

#80 - Bugfix to CellsByIdentities

Pull Request - State: closed - Opened by bbimber over 1 year ago - 1 comment

#79 - Fix/v5 vignettes

Pull Request - State: closed - Opened by AustinHartman over 1 year ago

#78 - Feat/variable features v5

Pull Request - State: closed - Opened by yuhanH over 1 year ago

#77 - Make layerdata return empty matrix instead of error

Pull Request - State: closed - Opened by Gesmira over 1 year ago

#76 - Fix FetchData cell order

Pull Request - State: closed - Opened by AustinHartman over 1 year ago

#75 - calcN generic

Pull Request - State: closed - Opened by yuhanH over 1 year ago

#74 - FeaturePlot BPcells

Pull Request - State: closed - Opened by yuhanH over 1 year ago

#73 - fix seurat options docs

Pull Request - State: closed - Opened by AustinHartman over 1 year ago

GitHub / mojaveazure/seurat-object issues and pull requests