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500lines

500 Lines or Less

academicpages.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

advanced-r-statistical-programming-and-data-models

Source Code for 'Advanced R Statistical Programming and Data Models' by Matt Wiley and Joshua F. Wiley

alignment-nf

Whole Exome/Whole Genome Sequencing alignment pipeline

arriba

Fast and accurate gene fusion detection from RNA-Seq data

awesome-bioinformatics

2018 Recommended Papers to Read in Bioinformatics as Voted by Bioinformaticians

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

bamsurgeon

tools for adding mutations to existing .bam files, used for testing mutation callers

batch-adjust-warning-reports

bioinf545

ATAC-seq lab for BIOINF545

bioinformatics

:microscope: Path to a free self-taught education in Bioinformatics!

bioinformatics-1

Bioinformatics Workflows

bioinformatics-resources

A curated list of resources for learning bioinformatics.

bioinformatics-with-python-cookbook-third-edition

Bioinformatics with Python Cookbook, Third Edition

bioinformaticsprojectunisa2017

A project developed for the bioinformatics course at the University of Salerno 2016/2017. The goal of the project was to develop a classifier, based on pathways, to identify subclass of patients affected by tumors. The proposed methodology is divided into four steps: (i) Dimensionality reduction: since the gene expression data is high dimensional the DFP algorithm was used to identify the discriminant genes (ii) Pathways identification: the enrichment analysis is used to identify those biological pathways (KEGG or Reactome) that are statistically represented by the genes identified in the previous step (iii) Classification of the patients based on SVM: for each pathway a linear SVM is trained in cross validation. The most relevant genes are also identified. (iv) Graphical representation: a graph is construct to represent the pathways relationships The code was developed in R and Python.

blogdown

Create Blogs and Websites with R Markdown

brcarepred

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

c3

cbioportal

cBioPortal for Cancer Genomics

cheatsheets

RStudio Cheat Sheets

chip-seq-analysis

ChIP-seq analysis notes from Tommy Tang

circexplorer

A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, Cell (2014), 159:134-147)

circlize

Circular visualization in R

codebase

Code depository for papers

codex-nf

Pipeline for copy number variant calling from Whole Exome sequencing data using CODEX

complexheatmap

make complex heatmaps as well as self define annotation graphics

cs-video-courses

List of Computer Science courses with video lectures.

dailycode

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.