Davide Cittaro

Unbuffered output

1

I'm running some codon generated executables in batch mode and I realized it sends to stdout just as Python (kind of expected), that is a buffered output. I know in...

cmultRepl implementation

4

Hi all, lately I had to implement the `cmultRepl` function from R package zCompositions in python. The original source (in R) is [here](https://rdrr.io/cran/zCompositions/src/R/cmultRepl.R), I'm attaching the python version to this...

Syntax for 3-reads, paired end technology?

2

Hello, I am processing some DBiT-seq data (but the I guess the same applies to any combinatorial barcoding strategy) in which the R2 is composed by a spaced cell barcode,...

Wrong file loaded when building new SpatialData

2

I am working with some data with many `.h5ad` files stored in the same directory. Whenever I create a new `SpatialData` object I specify the path to the correct `AnnData`...

There's a hidden function to plug a block state into `adata.uns` slot (`scs._utils.plug_state()`). Unfortunately it has not been updated (yet) and should not be used, as it breaks everything.

Not a good issue here: although one single state can typically fit in memory, multiple states are instantiated (default 100). Sometimes you don't have enough memory to fit them and...

Handling zeros

2

Hello, I was applying `propr`-derived code on some scRNA-seq data and I got some results that prompted me to investigate the expression level of some interesting genes. Due to the...