MartaBenegas

kallisto bustools with reference transcriptome

5

Dear team, I'm a little bit confused about the build index step. The manual says that it builds a transcriptome index but needs as input a genomic fasta and a...

I've followed the Seurat's [PBMC tutorial](https://satijalab.org/seurat/articles/pbmc3k_tutorial.html) and, after running the clustering, I saved the results in a loom file using the `as.loom()` [method](https://satijalab.org/seurat/articles/conversion_vignette.html#converting-to-from-loom). Then, I tried to open the file...

Hi, I would like to have all the expression data of two lanes in one loom file, so I've tried the combine() function. This is the information of the two...

Integration + data correction

2

Hi Seurat Team! I know that this topic has been addressed in previous issues (#7976 , #5879 ) but I'm still confused about it. It has been discussed that the...

Dear QUAST team, I'm running QUAST v 5.2.0 inside a docker and testing it with the test data. I haven't managed to generate the Upper Bound Assembly: ``` root@246f1e3d414e:/data# python3...

Hi QUAST team! I've just started using QUAST and I was wondering if there's a way to save the plots in a text file. That is, tab files with the...

Dataset not found with LoadData but it is installed

6

Hi, I was trying to use the SeuratData package. I've installed the package, looked at the available data, and installed it with the "Dataset" name. However, I'm not able to...

problems installing hdf5r package

2

Hi, I'm trying to install the library on an AWS with Linux 4.14.173-137.229.amzn2.x86_64. Following the instructions, I've first typed `sudo yum install hdf5-devel` on the terminal and the predetermined version...

pbmc68k_reduced raw counts

1

Hi! I was playing with the [pbmc68k_reduced](https://scanpy.readthedocs.io/en/stable/generated/scanpy.datasets.pbmc68k_reduced.html) dataset and I saw that it has decimal values even in the "raw" matrix: ``` >>> adata.raw.X.data array([2.177, 2.177, 2.544, ..., 1.142, 2.255,...

Error in expr[i, ] : incorrect number of dimensions

1

Hi, I'm encountering different errors while running ROGUE. My data: https://drive.google.com/drive/folders/1ePMiDRiDg98yYqcJxNi0f5zzvtE90R2p?usp=sharing How I'm loading it: ``` library(anndata) library(nbHelpers) counts