any2fasta

Convert various sequence formats to FASTA

apcluster

apcluster_effector_leafdrop_510_filtered_lessthan5tpm

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

bigscale2

Framework for clustering, phenotyping, pseudotiming and inferring gene regulatory networks from single cell data

bioinformatics-workshop

RNA-seq Tutorial

buscador

Annotating LRR-RP and LRR-RK proteins

camera

This is the git repository matching the Bioconductor package CAMERA: Collection of annotation related methods for mass spectrometry data

cheatsheets

RStudio Cheat Sheets

cmonkey

cMonkey integrated biclustering algorithm - official

cmonkeynwinf

Network Inference for cMonkey output based on Inferelator and elastic-net

codonusagetoolkit

Toolkit to analyze codon usage bias

commonmz

A collection of common mz values found in mass spectrometry.

copilot

Single cell RNA-seq preprocessing tool for gene-by-cell matrices of UMI counts. It is recommended to use the raw spliced and unpliced counts matrices produced by scKB pipeline as the input of copilot.

cytoscape-automation

Collection of scripts that include programmatic io and control of Cytoscape

dan_power_analysis_master

data

Data and code behind the articles and graphics at FiveThirtyEight

data-visualisation-course

interactive data visualisation

deep-learning-with-r-notebooks

R notebooks for the code samples of the book "Deep Learning with R"

deeplearning-biology

A list of deep learning implementations in biology

deeplearninginfinance

deepredeff

predict effector protein

dgca

DGCA 2.0: Highly Parallel and Memory-efficient Differential Correlation analysis

dip-c

Tools to analyze Dip-C (or other 3C/Hi-C) data

download_ncbi_assemblies

Downloading NCBI assemblies using accessions

drmn

DRMN with multi-task learning regression

effectorp-2.0

Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0

extract-promoter-sequences

Extract sequences upstream of genes in a fasta file based on coordinates listed in a gff file.

gamete-small-rna

R Markdown files for analyses of rice small RNA, gene expression and DNA methylation

gggenomes

A grammar of graphics for comparative genomics

ggplot2-exts.github.io

A list of ggplot2 extensions