hogfeldt / transcov Goto Github PK
View Code? Open in Web Editor NEWA bioinformatics software for mapping coverage around transcription start sites
License: GNU General Public License v3.0
A bioinformatics software for mapping coverage around transcription start sites
License: GNU General Public License v3.0
When tail cutting it could be nice, if you could plot the distribution and see how different modes and cuts will change the distribution.
The new generation type will for each region create a matrix where columns are bp-pairs in the region and rows are fragment length. The matrices should be concatenated into a tensor
generator.py
callable from api.py
Add content to the tutorial
Plot could be a heatmap
Right now testing is being done manually by running the gwf workflow on a cluster this cost a lot of time and computing resources.
It would be nice if we had automated tests to make sure that stuff don't break, when new features are added. Especially because I'm relying on this code in a project.
The big problem here is that a real bam file is huge and testing will take hours, so it could be nice if some small toy bam could be created. This could also make the matrices small enough to fit in ram on an ordinary machine and make it possible to use a CI tool like Travis.
For safety it could be nice if collapse would take corresponding index files and assert that they are equal.
Since there have been some interest in using this tool for more than just looking at TSS, it would be nice if the generator could take a bed file as input, by doing this the preprocesser can avoided with a handcrafted bed file.
A bed file will also have the benefit that it simplifies the code because it defines stable end points.
api.py
Right now you have to be explicit when going from uint16 to uint32, it would be nice if we could just detect when the limit is nearly reached and the shift from uint16 to uint32 and only waste space when necessary.
Create a gwf workflow example, that shows how to run this on many bam-files in parallel
Add manipulation for cutting tails of the coverage distribution.
It would also be nice if to add a script for plotting the coverage distribution.
It would be nice if we had logging. So that for example if collapse was called with no or only one argument it would notify the user through logging.
Right now bam files should have overlapping read pairs merged into single reads, to be able to handle short fragments. This special handling of bam files should eventually be replaced with a handling that checks for overlaps and identify the correct start and end point.
Make the docstrings from the API module available in the API documentation
Write about how to install the software:
Release
Write about Conda
Write about Pip
Write about the motivation for making this module and the overall idea on how the workflow works and how data is structured and flows
Motivation
Workflow and Data structure
The tss file should have a header telling what each column denotes
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.