bpnet
bpnet copied to clipboard
kundajelab
Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
(I'm using the bpnet conda environment, git commit de99967aa5) In bpnet/docs, ``` make build mkdir -p theme_dir/img/ipynb/ ./render_ipynb.bash pydocmd build make: pydocmd: Command not found make: *** [Makefile:13: build] Error...
Hello, I am a graduate student from the Luca/Pique-Regi lab and I'm trying to install leidenalg to ultimately run BPNet. I am using a Google Colab environment with Python 3.6....
Dear developers, This message comes from a very confused graduate student. Briefly, I'm trying to adopt the bpnet framework to my ATAC and Dnase-seq data (to avoid eyeballing motif scan...
I'm interested in viewing the `hyp_impscores` of the BPNet outputs, as seen in line 5, row 2 of [this document](https://github.com/kundajelab/tfmodisco/blob/master/examples/H1ESC_Nanog_gkmsvm/TF%20MoDISco%20Nanog.ipynb). First, I'm able to view the standard contribution scores using...
Hi, I was trying to follow the end-to-end bpnet pipeline on google colab and had several installation problems I was hoping you could shed light on. ERROR: Cannot install bpnet==0.0.1,...
Hi, I get the error below when trying to create the conda env for bpnet. I get a similar error using either method in the git README. I can install...
Hi there, I am currently trying to train BPNet on some human ChIP-seq data we have for an RNA Pol III transcription factor. We have multiple cell lines that I...
Hi, I am running Bpnet with 3 added input channels (in addition to the one hot input). These channels are the following bigwig files: [NT2 RNA Seq rep 1](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1720622), [NT2...
We're having a problem with permissions during installation. I was wondering if the code is being blocked for download right now ("failed" message on README page). If so, do you...
Hoo boy. Got a rough one. I'm trying to run BPNet on chemical mapping data, and it gets to epoch one before it crashes. It doesn't even crash cleanly. There's...
Metadata
Owner
Metadata
Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them