bitcometz issues

Results 23 issues of


                                            bitcometz

Schraivogel_2020.ipynb is not complete?

hello, I try to generate the Schraivogel_2020.h5ad according to the following notebook: https://github.com/theislab/sc-pert/blob/main/datasets/Schraivogel_2020.ipynb It seems it is not complete: ```python sc.pp.neighbors(adata) sc.tl.umap(adata) ``` Could you help with this problem ?...

TypeError: SPECTRA_Model.train() got an unexpected keyword argument 'label_factors'

hello, thanks for this great tool !!! I run this tool with CPU successefully but failed with GPU: ```python #import packages import numpy as np import json import scanpy as...

is daccordcontig suitable for the error correction with ONT data?

Hello, I have used the daccordcontig to do the error correction of scaffolds with PacBio reads, and it works really well, for example, the BUSCO assessment usually achieve above 90%....

Assertion `escore <= std::numeric_limits<uint32_t>::max()' failed

Hello, an another error in the other project : daccordcontig: ./HandleContext.hpp:3263: void HandleContext::operator()(std::ostream&, std::ostream&, const string&, const libmaus2::dazzler::align::BinIndexDecoder&, uint64_t): Assertion `escore

[E] parallel loop failed in HandleContext

Hello, I run daccordcontig and got some error information: [E] tid=24 [E] aread=6 bread=1782107: [16116800,16116843) [58230,58251) e=22 expected 21 ...... [E] tid=26 [E] aread=6 bread=1782107: [16116800,16116843) [58230,58251) e=22 expected 21...

some questions about the usage of 'split_dis'

Hello, I think 'split_dis' is a great idea and I want to use it to help me get better genome assembly, for example, to generate more complete repeat region, but...

Few results for menr.pkl in the 10x multiome pbmc Tutorial

Hello, thanks for this great tool !!! I try to redo the [10x multiome pbmc Tutorial](https://scenicplus.readthedocs.io/en/latest/pbmc_multiome_tutorial.html#Motif-enrichment-analysis-using-pycistarget) After I run the previous steps and I download the file and run: ```python...

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