denvercal1234github / scrnaseqpipeline Goto Github PK
View Code? Open in Web Editor NEWThis project forked from tallulandrews/scrnaseqpipeline
Various scripts for scRNAseq analysis
This project forked from tallulandrews/scrnaseqpipeline
Various scripts for scRNAseq analysis
This is a collection of scripts I use (or have used in the past) to process scRNASeq data. They are free to use by anyone else for any purpose, but come with no assurances or guarantees of correctness or functionality. The general workflow is as follows: 0 : Create the appropriate genome for the dataset, and obtain the read files & initial QC - Building mapping indexes generally requires ~30Gb of memory for a mouse-sized genome 1 : Split the files by well (cell), Trim reads as appropriate based on QC 2 : Map the reads to the genome 3 : Clean up mapping output & remove duplicates 4 : Mapping QC 5 : Quantify expression 6 : Assemble expression matrix Finished Pipelines: 00_Kallisto_For_SmartSeq.readme = Smartseq2 + Kallisto (no UMIs) Brief Descriptions of Useful files: 0_Extract_barcodes_from_BAM.sh : open the first line of each BAM file and find the barcode (tagged with BC:) - for matching up metadata.
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.