Peter Hickey

Small suggestion for sc3_prepare() documentation

1

Hi, Thanks for your work developing **SC3**! It might be worth noting that `sc3_prepare()` adds the `sc3_gene_filter` column to `rowData(object)` if `gene_filter = TRUE` (in addition to creating and populating...

WISH: Add colSums2() and rowSums2() with mode support

3

Opening a new issue for https://github.com/HenrikBengtsson/matrixStats/issues/82#issuecomment-297580797 I'd like if `matrixStats::rowSums2()` and `matrixStats::colSums2()` supported a `mode` argument, as implemented in `matrixStats::sums2()`. Dummy example: ``` r # Toy data x int [1:5,...

WISH: col/rowCounts but for inequalities

2

We have `rowCounts(x, value = 10)` as an efficient version of `rowSums(x == 10)`. It'd be neat to have similarly efficient versions of `rowSums(x > 10)`, `rowSums(x >= 10)`, `rowSums(x

BUG: weightedVar() returning incorrect (including negative) values

14

Hi Henrik, I encountered a situation where `matrixStats::colWeightedSds()` was giving me `NaN` variances. After doing some digging it appears this is due to `matrixStats::weightedVar()` returning negative variance estimates. Here's a...

Feature request: Re-analysing a user-specified subset of data

2

It would be great if it were possible to select a subset of cells and re-analyse that subset. E.g., In a dataset of PBMCs, select all 'B cells' (based on...

Reading `raw` data and differences between Python and R reader

6

Thanks for making it possible to read `h5ad` files into R. I had a few issues/questions after trying to get the raw count matrix from a public `h5ad` file. Some...

Exposing h5repack?

1

Is it possible to expose the `h5repack` tool (https://support.hdfgroup.org/HDF5/doc/RM/Tools.html#Tools-Repack) for use within R? Background: I deleted a dataset from a HDF5 file and learnt that doesn't actually make the HDF5...

`combineCols()` errors when called via `do.call()` with a named list of objects to be combined

5

Please note that this may properly be a bug report for **S4Vectors** or **SumarizedExperiment**, so I'm tagging @hpages, but I encountered it when applying `combineCols()` via `do.call()` to a list...

Coercion from *SingleCellExperiment* to *SummarizedExperiment* loses rownames

1

``` r suppressPackageStartupMessages(library(SingleCellExperiment)) example(SingleCellExperiment, echo = FALSE) rownames(sce) [1] "Gene_1" "Gene_2" "Gene_3" "Gene_4" "Gene_5" "Gene_6" #> [7] "Gene_7" "Gene_8" "Gene_9" "Gene_10" "Gene_11" "Gene_12" #> [13] "Gene_13" "Gene_14" "Gene_15" "Gene_16" "Gene_17"...