GDC Data Portal: Data from several cancer studies (including TCGA)
gnoMAD: aggregation of exome and genome sequencing data from unrelated individuals to assess allele frequencies across populations.
GTEX Portal: The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation.
DoCM: Database of Curated Mutations
Cancer Genetics Web: Gene-mutation database
COSMIC: Catalogue of Somatic Mutations in Cancer
ClinVar: Genomic variation + human health
Harmonize: Integrated knowledge about genes and proteins. Helpful for expression of various genes in cell lines.
PTMCosmos: PTMcosmos is a database of known Post-Translational Modification (PTM) sites as well as novel sites detected in the Clinical Proteomic Tumor Analysis Consortium (CPTAC) experiments. It also shows the cancer mutations overlapping a PTM, which can potentially disrupt the PTM’s function (e.g., cell signaling).
GDC Data Portal: Bam, bam slice, clinical info, other important info for TCGA samples
cBioPortal: The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.
GEPIC: Gene expression profiling interactive analysis
Pancan Atlas Publication Data: RNA, RPPA, Methylation, miRNA, Copy Number, Mutations, Clinical Data, Pathway etc.
Xena Functional Genomics Explorer: explore functional genomic datasets for correlations between genomic and/or phenotypic variables - includes TCGA, GTEX
ExPASY: Bioinformatics Resource Portal
Cancer Genome Interpreter: cancer drivers + genomic biomarkers
Expression Atlas: Gene expression across species and biological conditions
iGenomes: ready to use reference sequences and annotations from Illumina
Drug Bank: A unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information.
PharmGKB:
Uniprot: provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
RCSB Protein Data Bank: an information portal to biological macromolecular structures
RBPmap: Mapping binding sites of RNA Binding Proteins.
SFmap: Motifs analysis and prediction of splicing factors.
MotifMAP-RNA: Comprehensive maps of candidate regulatory elements (RBPs binding sites etc). + ChIP-Seq data
SpliceAid2: a database of human splicing factors expression data and RNA target motifs
SpliceAidF: a dabase of human splicing factors and their binding sites (2013)
MAJIQ: MAJIQ and Voila are two software packages that together detect, quantify, and visualize local splicing variations (LSV) from RNA-Seq data.
GeneMarkeR: A Database and User Interface for scRNA-seq Marker Genes
PanglaoDB: We collect and integrate data from multiple studies and present them through a unified framework.
CellMarker2.0: Manually curated cell markers in human/mouse data.
DISCO: Deeply Integrated human Single-Cell Omics data
Awesome Single Cell: Repository of lots of single-cell related tools
WASHU Genetics Course (Bio5488)
Grantome
Equity reading list from Bhalla Lab
PubPeer: Online Journal Club
Confluence
To Install Pymol -> First download Homebrew -> then run 'brew install homebrew/science/pymol'
Quality control of alignment data: http://qualimap.bioinfo.cipf.es/, http://multiqc.info/
D3 Visualization - https://github.com/d3/d3/wiki/Gallery
SunburstR - Source Code - R Documentation - Example data input, Example data input 2- Actually helpful for running with input data -