mnnpy

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I was wondering about the reproducibility of the batch correction and haven't found anything in the documentation. Ideally, I would like to be able to run a batch correction on...

sophiamaedler

Not be able to install

1

I am trying to install mnnpy on MacOS sierra, however I was not able to install, error message is as following: clang: error: unsupported option '-fopenmp' error: command 'gcc' failed...

ivonyao

Error during cosine normalization step

5

Hello, First, thank you for this awesome implementation of MNN in python , great work! I was looking forward to try it and compare it with Seurat's CCA on my...

LucasESBS

comput_angle=True generates error

1

Hi, I wanted to obtain the angles and the following error is produced: ``` multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/n/app/python/3.6.0/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True,...

chlee-tabin

input data type

5

what kind of data can be used as mnnpy's input ? log(counts), log(CPM) or others?

wangjiawen2013

mnnpy returns

3

Dear Chriscainx, I am using mnnpy to correct my single cell data. Before this, I compared mnnpy with scran's mnnCorrected function with two matrix (B1

wangjiawen2013

out_batches not being set in transform_input_data() with cos_norm_out=False

2

Hello, For whatever reason, I feel more comfortable running `mnn_correct()` with `cos_norm_out` set to False. As such, I tried to do it this way, and got an error about `out_batches`...

ktpolanski

no response at Performing cosine normalization...

5

Hi, thank you for this awesome implementation of MNN in python , it's a great work! when I use MNN to my data (~30000 genes * ~ 60000 cells) with...

zacharylau10

Cosine Normalization error

8

corrected = mnnpy.mnn_correct(D1, D4, var_subset=Gene_list, batch_categories =["Day1","Day4"]) Performing cosine normalization... multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/projects/academic/gbcstaff/utils/anaconda/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "/projects/academic/gbcstaff/utils/anaconda/lib/python3.6/multiprocessing/pool.py",...

julien-kann

Cython module _utils not initialized. Fallback to python.

2

Hi Chris! When I executed `import mnnpy` I got ``` ~/PyCharm.app/Contents/helpers/pydev/_pydev_bundle/pydev_import_hook.py:19: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be...

stashkov