Songpeng Zu

From the document website: https://www.flycheck.org/en/latest/index.html, I did not find the support for ESS/R language. But Flycheck actually support it in the codes.

What do you mean exactly "rope and ropemacs should be in your PYTHONPATH for this to work" ?

Variational inference in cmdstanr missing importance_resampling that is in rstan

14

Under this link: https://mc-stan.org/cmdstanr/reference/model-method-variational.html , there are no parameters for "important_resampling", "keep every" in rstan (https://mc-stan.org/rstan/reference/stanmodel-method-vb.html) ? - From my understanding, cmdsranr should support the newest stan compared with rstan....

knowing the initial values for sampler even I don't set up the initials

2

I can get the initial values for sampler (or variational inference, or optimization) using the function `init()` if I set the initial values. But how can I get the initial...

Hi there, Thank you so much for providing this great tools! Even I am using Emacs >= 29.1, I find using tree-sitter as a minor mode has its own advantages....

BUG: some tree-sitter repos are quite old, like r

5

Hi there, When I use tree-sitter-r, I notice that the version is pointed to a very old one (2022), while the source of the[ tree-sitter-r ](https://github.com/r-lib/tree-sitter-r) has been updated recently....

hard to understand about the description in filter features.

1

Hi Kai, Here is the description of filter features: ``` If inplace = False, return a boolean index mask that does filtering, where True means that the feature is kept,...

scanpy AnnData to snapatac2 AnnData: cannot read csr_matrix

2

Hi Kai, I have an anndata.AnnData, I can generate the snapatac2.AnnData as followed ``` # ann is an anndata.AnnData sa2ann = snapatac2.AnnData(filename = "tmp.h5ad", X = ann.X) ``` When I...

the description of read_mtx is not clear

6

Hi Kai, I found that the description of read_mtx is not clear. 1. obs_names: File that stores the observation names. - obs_name_file would be better, otherwise, it's hard to know...

Add support to convert AnnData to Seurat v5

6

Hi Kai, https://github.com/beyondpie/CEMBA_wmb_snATAC/blob/c48737ddf360519231721b63cc81a0fc75d83cca/02.integration/src/main/R/annToS5.R#L36C9-L36C9 Here is how I did the transformation for gmat. We can also think about how to transform AnnData to Signac object, where they support cicero and other...