Ecosyste.ms: Issues

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GitHub / ltla/scuttle issues and pull requests

#32 - downsampleMatrix returns sparse when it should return dense result

Issue - State: open - Opened by mschubert about 2 months ago - 3 comments

#30 - Adding subsets used to SCE

Pull Request - State: closed - Opened by llrs 5 months ago - 4 comments

#29 - Adding subsets from addPerCellQC to rowData

Issue - State: closed - Opened by llrs 5 months ago - 2 comments

#28 - discrepancy between addPerCellQC's sum & colSums

Issue - State: closed - Opened by HelenaLC 6 months ago - 2 comments

#27 - empty heatmap (aggregateAcrossCells)

Issue - State: closed - Opened by Elena983 10 months ago - 5 comments

#25 - summarizeAssayByGroup output has NULL colnames when ids is a DataFrame

Issue - State: closed - Opened by alanocallaghan over 1 year ago - 2 comments

#24 - calculateAverage() throw error 'rowMeans' : size factors should be positive

Issue - State: open - Opened by boutrys over 1 year ago - 1 comment

#23 - Fix typo in docs

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

#22 - aggregateAcrossCells with `statistics = "median"` produces warnings

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

#21 - Adding alias to exprs_values argument

Issue - State: closed - Opened by antagomir almost 2 years ago - 3 comments

#20 - Factors in subset2index

Pull Request - State: closed - Opened by alanocallaghan almost 2 years ago - 3 comments

#19 - Add swap_rownames to makePerCellDF

Pull Request - State: closed - Opened by samuel-marsh about 2 years ago

#18 - makePerCellDF using alt rowData Column

Issue - State: closed - Opened by samuel-marsh about 2 years ago - 4 comments

#17 - aggregateAcrossCells() no longer works over multiple assays in SCE

Issue - State: open - Opened by AnnaAMonaco over 2 years ago - 3 comments

#16 - How to recover gene expression used for scran::pairwiseTTests()

Issue - State: open - Opened by ewijaya over 2 years ago - 1 comment

#15 - No. of discarded cells do not add up?

Issue - State: open - Opened by shaln almost 3 years ago - 1 comment

#14 - unable to install scuttle

Issue - State: open - Opened by wonliy almost 3 years ago - 14 comments

#13 - makePerCellTbl

Issue - State: open - Opened by robertamezquita over 3 years ago - 2 comments

#12 - logNormCounts - log transformation with different log base?

Issue - State: open - Opened by JPGranizo over 3 years ago - 3 comments

#11 - no slot of name "subdata" for this object of class "TENxMatrixSeed"

Issue - State: open - Opened by janinemelsen over 3 years ago - 1 comment

#9 - Size factors allowed to be zero even when positive=TRUE

Issue - State: closed - Opened by alanocallaghan almost 4 years ago - 1 comment

#8 - Suggestion related to cluster IDs given #7

Issue - State: closed - Opened by lcolladotor almost 4 years ago - 2 comments

#7 - What should the minimum colSums(counts) be for overcoming rescaling = 0 results?

Issue - State: closed - Opened by lcolladotor almost 4 years ago - 4 comments

#6 - Typing out the three QC commands is a pain

Issue - State: closed - Opened by LTLA almost 4 years ago - 1 comment

#5 - Error: object ‘I’ is not exported by 'namespace:S4Vectors'

Issue - State: closed - Opened by cytogil almost 4 years ago - 3 comments

#4 - Failed to find a rowRanges() method for SingleCellExperiment objects

Issue - State: closed - Opened by YifeiSheng almost 4 years ago - 1 comment

#3 - Column names of perCellQCMetrics output vary depending on how use.altexps supplied

Issue - State: closed - Opened by PeteHaitch almost 4 years ago - 1 comment

#2 - Migrate all code to use beachmat v3 with block processing.

Pull Request - State: closed - Opened by LTLA about 4 years ago

#1 - [REQ] Support of medians by aggregateAcrossCells()

Issue - State: closed - Opened by HelenaLC over 4 years ago