maxATAC

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import error _OrderedEnqueuer_ tensorflow.keras.utils

6

Hi, While I was installing maxATAC with Conda `conda create -n maxatac -c bioconda python=3.9 samtools wget bedtools ucsc-bedgraphtobigwig pigz` `pip install maxatac` # Test installation `maxatac -h` I noticed...

martinezvbs

`maxATAC` prepare with sc 10X ATAC

2

Hi! I am trying to run maxATAC on `scATAC` data from 10X system. I am running `maxatac preapre` and pointing the function to my fragments file that ends with `.tsv.gz`...

daccachejoe

Change Path for

1

Hi, I was wondering what I need to adjust and to which constants.py I need make the adjustment to change the location of reference data? I am working on a...

Elfaba

Removed certain flags (-n, --name) that do not yield expected behavior and added one flag (--tf) that can also specify TFs.

ANRudrapatna

Numpy compatibility for Tensorflow 2.5 and SHAP in interpreting analysis jobs

2

We have this conflict between tensorflow and shap, where tensorflow 2.5 cannot work with numpy >=1.20.0 and shap is compiled with numpy API version 0xe (numpy >=1.20.0 I believe, the...

XiaotingChen

pyBigWig values method does not take argument numpy=True

1

https://github.com/MiraldiLab/maxATAC/blob/83cd5d2b95037cb2b100f72c0545e244336de72c/maxatac/utilities/normalization_tools.py#L47 ```bash File "/gpfs/home/.conda/envs/maxatac/lib/python3.9/site-packages/maxatac/utilities/genome_tools.py", line 236, in chromosome_blacklist_mask return blacklist_bigwig_stream.values(chromosome, TypeError: values() takes no keyword arguments ``` Same format in another file: https://github.com/MiraldiLab/maxATAC/blob/83cd5d2b95037cb2b100f72c0545e244336de72c/maxatac/utilities/genome_tools.py#L239 Removing numpy=True seems to resolve the issue.

tanjimin

Error on running predict: could not load dynamic library for tensorflow

1

Hi Tareian, It's me again, after fixed prepare function on samtools and bedGraphToBigWig by reinstallation, the predict function got some "cannot open shared object file: No such file or directory"...

timothykoala

We currently only produce plots for `train` and `benchmark`. It would be nice to add some additional plotting functions. - [ ] Plot bar plot of max values across chromosomes...

tacazares

tacazares

We want to test out which model parameters are best for predicting TF binding - [ ] Kernel size - [ ] Filter number - [ ] Receptive Field -...

tacazares