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A list of useful bioinformatics resources

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This is a collection of bioinformatics tools I have sourced from recent literature, organized by topic. I have not used most of these tools.

Table of Contents

Clinical data

EHR

Data Management

Data Sets

Discovery

When looking for a bioinformatics tool for a specific application:

Genomics

General Information

Algorithms

Assay Design

Candidate Prioritization

Databases

Data Formats

Functional Enrichment/Ontology

GWAS/QTL

Microarray

Motif/TFBS

Network Analysis

Population genetics

Prediction

Security

Sequencing Protocols

Simulation

Variant annotation

Sequence Analysis

General-purpose

Demultiplexing

QC

ChIP-seq

Chromatin accessibility

Chromatin Interactions

DNA

Footprinting

Metagenomics

Methylation

MNase-seq

Nanopore

RNA

Single-cell

Somatic

Integrated Methods

General Programming Resources

C/C++

R

Find packages

Database

  • MonetDB - embeddable column-store DB with R integration (MonetDB.R)

Data Cleaning

Reporting

Misc

Python

HPC

Command Line (OSX/Linux)

Databases

Reproducibility/Containerization

Building Pipelines

Software Distribution

Other

Statistics/Machine Learning

Methods/algorithms

Python

Deep Learning

Web APIs

Data Sets

Text classification

Visualization

Networks

Phylogenetic trees

R

ggplot2

Plot Types

Data Types

Interactive

Python

Javascript

Examples

Publication/Archiving

Code/Data sharing

Journals

Writing

Promising methods without software implementation

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A list of useful bioinformatics resources

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