mnnpy

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Index out of bounds, Looking for MNN not working.

1

I am trying to perform MNN correction for two different AnnData on Google Collabs. I sub-setted both the data to 1000 observation to check if it works or not. I...

Ayush-Praveen

mnnpy fails to import with latest version of numba

5

mnnpy (version 0.1.9.5) fails to import when using the latest version of numba (0.44.0). Rolling back to the previous version of numba (0.43.1) fixes this issue. Most of the error...

sinclaircooper

IndexError

3

I get the following error when using MNN with 4000 genes, but do not get it when testing on 100 genes. This is with the newest numba version (0.47.0) ```...

adamgayoso

Does not install on macOS

13

Tried installing this for scanpy, as recommended (`pip install mnnpy`), on a macOS High Sierra (v10.13.4) within a Miniconda environment, but it returns an error: ``` clang: error: unsupported option...

veghp

mnnpy.mnn_correct returning a Tuple

1

Here is a reproducible code for the error: ``` import scanpy as sc import scanpy.external as ice from itertools import cycle pbmc = sc.datasets.pbmc68k_reduced() pbmc_corrected = mnnpy.mnn_correct(pbmc, batch_key="phase", save_raw=True) ```...

Gpasquini

I have only numpy array data: cells * genes, labels, batches How can I use this with such data?

noobCoding

Why do the variances of the correction vector need to be adjusted and how does that work? I tried finding details about it in the paper / SI materials but...

atarashansky

Hi, thank you for implementing this algorithm in Python! Also please forgive me if I am making an obvious mistake here. But I am wondering whether the correction_vectors are being...

dylkot

Hi, I am working with MNN, and was wondering why in the paper sometimes the union of the highly variable genes (HVGs, calculated within batches) is used, whereas other times...

LisaSikkema

error when set cos_norm_out=False

3

>>> corrected = mnnpy.mnn_correct(a,b,var_index=gene, var_subset=hvgs, batch_categories = ["A", "B"], cos_norm_out=False) Inputs are AnnData objects, var_index ignored. Performing cosine normalization... Traceback (most recent call last): File "", line 1, in File...

yupingz