Useful links
Library and database
POSTAR3 (POST-translational regulation (e.g. RNA-Binding Protein's Targets)): http://111.198.139.65/index.html
ChIP-Atlas (comprehensive db for epigenetic datasets (e.g. ChIP, DNase, ATAC); peaks, target genes, colocalization, enrichment) https://chip-atlas.org/target_genes
CHEA3 (predict TF enrichment from a gene list)
human super-enhancer database and sister database
Reference scRNA-seq datasets/"atlases":
Cell x gene (many datasets): https://cellxgene.cziscience.com/
Mouse: https://tabula-muris.ds.czbiohub.org/
Human: https://tabula-sapiens-portal.ds.czbiohub.org/
Human Immunology Project Consortium (HIPC): http://www.hipc-dashboard.org/
(including all scRNA datasets)
https://www.encodeproject.org/ (Data resource)
Gene Ontology::
http://current.geneontology.org/products/pages/downloads.html
Transcription factor ontology:
http://bioinfo.life.hust.edu.cn/AnimalTFDB/#!/
http://humantfs.ccbr.utoronto.ca/download.php
Enrichr: gene enrichment
OmniPath: available in R, Python, and via webtool. Database of:
- Protein-protein, TF-target, miRNA-mRNA interactions
- Enzyme-PTM relationships
- Protein complexes
- Annotation of protein function, structure, localization, expression
- Intercellular communication roles of proteins
Documentation for webtool: https://github.com/saezlab/pypath/blob/master/webservice.rst
SEdb: the comprehensive human Super-Enhancer database
ENdb: an experimentally supported enhancer database for human and mouse
SEanalysis: a web tool for super-enhancer associated regulatory analysis
ATACdb: a comprehensive human chromatin accessibility database
LncSEA: a comprehensive human lncRNA sets resource and enrichment analysis platform.
RBPmap: binding sites for RNA-binding proteins
TRCirc: a resource for transcriptional regulation information of circRNAs
TRlnc: a comprehensive database of human transcriptional regulation of lncRNAs
VARAdb: a variation annotation database for human
gnomAD: variant annotation from GTEx, TOPMED, and other GWAS published by Broad
Immunology Database
GPX-Macrophage Expression Atlas
immune related networks - systems biology.
innate immune system interactions, systems biology
NGS
the edX learning platform, founded by Harvard and The Massachusetts Institute of Technology (MIT)
(UNIX, Genomics, Phylogenetics, Programming, etc)
R Graphing Resources
ggsci: color palettes for publications
A link to a useful stackexchange post with bright colors for categorical variables: https://graphicdesign.stackexchange.com/a/157153
R Graph Gallery: helpful tutorials for different types of graphs
cookbook-R: tutorials for changing graph parameters in ggplot2
programming with dplyr: essential for writing functions where you pass arguments to ggplot2
setworks: web app to make overlapping intersection/network plots
Restriction Enzymes
NEB tool for optimizing single and double digest buffers: https://nebcloner.neb.com/#!/redigest
NEB chart of enzyme activities in different buffers and methylation sensitivity: https://www.neb.com/en-us/tools-and-resources/usage-guidelines/nebuffer-performance-chart-with-restriction-enzymes
NEB list of isoschizomers: https://www.neb.com/en-us/tools-and-resources/selection-charts/isoschizomers