Giter Club home page Giter Club logo

couplenmf's People

Contributors

wanwenzeng avatar

Stargazers

avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar

Watchers

avatar

Forkers

biobenkj yanqiangli zorrodong indajuan taoliu yu1033704806 kfdk

couplenmf's Issues

关于peak_gene_100k_corr.bed文件 

你好，我现在打算运行这个程序，研究时不太理解输入的文件。
首先是peak_gene_100k_corr.bed这个文件的第三第四列是什么，数据是从哪里来的呢。我使用10X（https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/using/count）做单样本分析时数据其中的一个文件是peak_annotation.tsv，其中有一列是distance，跟你这个文件的第四列有些像。
还有就是PeakName.txt这个文件是怎样来的呢，我一开始以为是peak_gene_100k_corr.bed去重后的数据，发现不一致的。
如果有时间，希望解答一下~

Missing "RE_v2.bed" in pre-processing script

  • It's unclear what is RE_v2 refers to, in the pre-processing script
  • .bed and .bam files are used interchangeably in the README and the remaining scripts, creating some confusion

How to calculate A

Hi,

After reading your paper, I am interested in this method.
https://www.pnas.org/content/115/30/7723

I thought it was very advanced as a way to integrate two matrices that have neither rows nor columns in common.

By the way, the matrix A (Peak×Gene) in Equation (1) seems to be a pre-calculated matrix in this implementation , but what kind of calculation do you do to get it?

coupleNMF/coupleNMF.py

Line 44 in 116a5d4

parser.add_argument('-pe', type=argparse.FileType('r'), help='the location of pre-calculated peak-gene interactions')

I'm not familiar with the problem of penalized least-squares in equation (3), and I was wondering what kind of solver is used to solve it.
In particular, since the Frobenius norm contains a summation symbol, it seems to me that this model is different from general linear regression.

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.