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#bioinformatics #data-analysis #next-generation-sequencing

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README

awosome-bioinformatics

Abstract: A curated list of resources for learning bioinformatics. Some of this repo resources were collected by BioInstaller project. You can use BioInstaller to directly download the source code or database files, or fetch the meta information by BioInstaller::get.meta()$item.

Purpose:

Provide some of bioinformatics learning resources for beginners
Provide a profiling of bioinformatics

Field:

Next generation sequencing (NGS)
Bioinformatics Data Analysis

Table of content

Resources

- General - Journal - Sequencing Technology - Tools - Books&Tutorial - Paper

Skills
Organization
Institute
People
Blog
Contributors

Resources

General

Journal

Bioinformatics

Genomics

Proteomics

Sequencing Technology

This section mainly copied from enseqlopedia.

Thanks this work: Hadfield, J. & Retief, J. A profusion of confusion in NGS methods naming. Nat Methods 15, 7-8 (2018).

RNA Sequencing Methods

Low-Level RNA Detection

- CEL-Seq - CirSeq - CLaP - CytoSeq - Digital RNA Sequencing - DP-Seq - Drop-Seq - Hi-SCL - InDrop - MARS-Seq - Nuc-Seq - PAIR - Quartz-Seq - scM&T-Seq - SCRB-Seq - scRNA-Seq - scTrio-seq - Smart-Seq - Smart-Seq2 - snRNA-Seq - STRT-Seq - SUPeR-Seq - TCR-LA-MC PCR - TIVA - UMI - 5C - Div-Seq - FRISCR - TCR Chain Pairing - AbPair

RNA Modifications

- ICE - MeRIP-Seq - miCLIP-m6A - Pseudo-Seq - PSI-Seq

RNA Structure

- CAP-seq - Cap-Seq - CIP-TAP - PARS-Seq - SPARE - Structure-Seq/DMS-Seq - CIRS-Seq - icSHAPE - SHAPE-MaP - SHAPE-Seq

RNA Transcription

- 2P-Seq - 3'NT Method - 3P-Seq - 3Seq - 3′-Seq - 5′-GRO-Seq - BruChase-Seq - BruDRB-Seq - Bru-Seq - CAGE - CHART - ChIRP - ClickSeq - GRO-seq - NET-Seq - PAL-Seq - PARE-Seq - PEAT - PRO-Cap - PRO-Seq - RAP - RARseq - RASL-Seq - RNA-Seq - SMORE-Seq - TAIL-Seq - TATL-Seq - TIF-Seq - TL-Seq - 4sUDRB-Seq - CaptureSeq - cP-RNA-Seq - FRT-Seq - GMUCT - mNET-Seq

RNA-Protein Interactions

- AGO-CLIP - CLASH - CLIP-Seq or HITS-CLIP - DLAF - eCLIP - hiCLIP - iCLIP - miR-CLIP - miTRAP - PAR-CLIP - PIP-Seq - Pol II CLIP - RBNS - Ribo-Seq or ARTSeq - RIP-Seq - TRAP-Seq - TRIBE - BrdU-CLIP - HiTS-RAP - irCLIP

DNA Sequencing Methods

Protein-Protein Interaction

- PD-Seq - ProP-PD/PDZ-Seq

Sequence Rearrangements

- 2b-RAD - CPT-seq - ddRADseq - Digenome-seq - EC-seq - hyRAD - RAD-Seq - Rapture - RC-Seq - Repli-Seq - SLAF-seq - TC-Seq - Tn-Seq/INSeq - Bubble-Seq - NSCR - NS-Seq - Rep-Seq/Ig-Seq/MAF

DNA Break Mapping

- BLESS - DSB-Seq - GUIDE-seq - HTGTS - LAM-HTGTS - Break-seq - SSB-Seq

DNA Protein Interactions

- DNaseI Seq or DNase-Seq - Pu-seq - 3-C/Capture-C/Hi-C - 4C-seq - 5C - ATAC-Seq/Fast-ATAC - CATCH\_IT - Chem-seq - ChIA-PET - ChIPmentation - ChIP-Seq/HT-ChIP/ChIP-exo/Mint-ChIP - DamID - DNase I SIM - FAIRE-seq/Sono-Seq - FiT-Seq - HiTS-FLIP - MINCE-seq - MNase-Seq/MAINE-Sequcleo-Sequc-seq - MPE-seq - NG Capture-C - NOMe-Seq - ORGANIC - PAT-ChIP - PB\_seq - SELEX or SELEX-seq / HT-SELEX - THS-seq - UMI-4C - X-ChIP-seq

Epigenetics

- Aba-seq - BisChIP-Seq/ChIP-BS-Seq/ChIP-BMS - BSAS - BSPP - BS-Seq/Bisulfite-Seq/WGBS - CAB-Seq - EpiRADseq - fCAB-seq - fC-CET - fC-Seal - hMeDIP-seq - JBP1-seq - MAB-seq - MBDCap-seq/MethylCap-Seq/MiGS - MeDIP-Seq/DIP-seq - MIRA - MRE-Seq and Methyl-Seq - xBS-Seq - PBAT - redBS-Seq/caMAB-seq - RRBS-Seq - RRMAB-seq - TAB-Seq - TAmC-Seq - T-WGBS - BSPP - TBS

Low-Level DNA Detection

- Safe-SeqS - scAba-seq - scATAC-Seq (Cell index variation) - scATAC-Seq (Microfluidics variation) - scBS-Seq - scM&T-Seq - scRC-Seq - SMDB - smMIP - G&T-Seq - 5C - DR-Seq - G&T-Seq - MALBAC - MDA - MIDAS/IMS-MDA/ddMDA - scM&T-Seq - Drop-ChIP/scChIP-seq - Duplex-Seq - MIPSTR - nuc-seq/SNES - OS-Seq

Tools

Package management

Web Application Developement Framework

Web-based Service

Hiplot: a simple and user-friendly visualization platform for scientific data.
SeqBench: DNA/RNA/protein sequence analysis toolkit with batch processing and multi-tool workflow pipelines over whole FASTA files, plasmid/sequence visualization, primer design, restriction & cloning simulation, and CRISPR guide design; exposes an MCP server and REST API for AI agents.
UCSC
NCBI

- CDD

- COSMIC-3D: a comprehensive integration of cancer mutations with protein structure across the human genome and structural proteome, seeking to support the identification and characterization of protein targets for novel drug design in precision oncology

- Oncoprinter - MutationMapper

- Cistrome Data Browser - Cistrome Cancer - Chromatin Regulator Cistrome - TIMER

VarCards
superdrug2
MeDReaders
ECOdrug
rSNPBase3.0
MNDR
MSDD
funcoup
proteinatlas
DGIdb
Drugbank
InterPro
ncbi-biosystems
denovo-db
The Human Phenotype Ontology (HPO)
FANTOM
dbNSFP
regSNP-intron
RADAR
DARNED
REDIportal
LNCediting
EggNOG
MiSTIC
DTMiner
PDBFlex
Cancer3d
Dsysmap
CBS Prediction Servers
wANNOVAR: Public web service of ANNOVAR
Harmonizome: Search for genes or proteins and their functional terms extracted and organized from over a hundred publicly available resources
GDA: A web-based tool that combines NCI60 uniquely large number of drug sensitivity data with CCLE and NCI60 gene mutation and expression profiles
CLUE: Unravel biology with the world’s largest perturbation-driven gene expression dataset
CMAP: The Connectivity Map (also known as cmap) is a collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms that together enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes.
pssmsearch: a web application to discover novel protein motifs (SLiMs, mORFs, miniMotifs) and PTM sites
bammmotif: Bayesian Markov Models (BaMMs), a web server for de-novo motif discovery and regulatory sequence analysis
LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis
GeNets: a unified web platform for network-based genomic analyses
HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization
paintomics: a web resource for the pathway analysis and visualization of multi-omics data
kinact: a computational approach for predicting activating missense mutations in protein kinases
VAReporter: VAReporter can provide comprehensive annotation by integrating a wide variety of biomedical databases
SNPnexus: SNPnexus was designed to simplify and assist in the selection of functionally relevant Single Nucleotide Polymorphisms (SNP) for large-scale genotyping studies of multifactorial disorders
Oncoscape: an online open-access dataanalysis and visualization platform that empowers researchers and clinicians to discover novel patterns and relationships between linked clinical and molecular data
cellmarker: a manually curated resource of cell markers in human and mouse
awesome: a database of SNPs that affect protein post-translational modifications
hmdb: an online database of small molecule metabolites found in the human body, which facilitates human metabolomics research including the identification and characterization of human metabolites using NMR and MS
redoxdb: a curated database of protein oxidative modification
instruct: a database of 3D protein interactome networks with structural resolution
consensuspathdb: integrates interaction networks in Homo sapiens including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways
phosphonetworks: a database for experimentally determined kinase-substrate relationships
dbsno: protein S-nitrosylation (SNO) is a reversible post-translational modification (PTM) and involves the covalent attachment of nitric oxide (NO) to the thiol group of cysteine (Cys) residues. Given the increasing number of proteins reported to be regulated by this modification, S-nitrosylation is considered to act, in a manner analogous to phosphorylation, as a pleiotropic regulator that elicits dual effects to regulate diverse pathophysiological processes by altering protein function, stability, and conformation change in various cancers and human disorders
hpdi: Human Protein-DNA Interactome (hPDI)
islandviewer: an integrated interface for computational identification and visualization of genomic islands
appris: a system that deploys a range of computational methods to provide annotations of alternative splice isoforms and identify principal isoforms for vertebrate species
rbpdb: a collection of RNA-binding proteins linked to a curated database of published observations of RNA binding
type2diabetesgenetics: providing data and tools to promote understanding and treatment of type 2 diabetes and its complications
pepquery: a peptide-centric search engine for novel peptide identification and validation
Gene Info eXtension (GIX): a browser extension that allows you to retrieve information about a gene product directly on any webpage simply by double clicking an official gene name, synonym or supported accession.
cancermine: a literature-mined resource for drivers, oncogenes and tumor suppressors in cancer.
gpcrdb: contains data, diagrams and web tools for G protein-coupled receptors (GPCRs). Users can browse all GPCR structures and the largest collections of receptor mutants. Diagrams can be produced and downloaded to illustrate receptor residues (snake-plot and helix box diagrams) and relationships (phylogenetic trees). Reference (structure) structure-based sequence alignments take into account helix bulges and constrictions, display statistics of amino acid conservation and have been assigned generic residue numbering for equivalent residues in different receptors.
FPbase: a free, open-source, web-based, communityeditable database for fluorescent proteins (FPs) and their properties.
Image Data Resource (IDR): Image Data Resource (IDR) is a public repository of image datasets from published scientific studies, where the community can submit, search and access high-quality bio-image data.
Allen Brain Atlases and Data: The Allen Institute for Brain Science uses a unique approach to generate data, tools and knowledge for researchers to explore the biological complexity of the mammalian brain. This portal provides access to high quality data and web-based applications created for the benefit of the global research community.
Allen Cell Explorer: a python-based, open-source toolkit that combines classic 3D image segmentation with artificial intelligence to detect cellular structures.
Mitotic Cell Atlas: Provides a comprehensive and quantitative 4D model of the mitotic protein localization network in a dividing human cell. Mitotic Cell Atlas is an integrated experimental and computational framework that provides a standardized yet dynamic spatio-temporal reference system for the mitotic cell. It can be used to integrate quantitative information on any number of protein distributions sampled in thousands of different experiments.
Broad Bioimage Benchmark Collection: a collection of freely downloadable microscopy image sets. In addition to the images themselves, each set includes a description of the biological application and some type of "ground truth" (expected results).
Cell Image Library: a repository for images and movies of cells from a variety of organisms. It demonstrates cellular architecture and functions with high quality images, videos, and animations. This comprehensive and easily accessible Library is designed as a public resource first and foremost for research, and secondarily as a tool for education. The long-term goal is the construction of a library of images that will serve as primary data for research.
Mitocheck: the goal of this resource is to integrate information on cellular functions of human genes while also giving access to supporting information such as microscopy images of phenotypes. Although its primary focus is on the biology of mitosis, the resource also integrates data relevant to many other cellular functions.
ssbd: Systems Science of Biological Dynamics (SSBD) database provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, gene expression nuclei, etc. Quantitative biological data and microscopy image are collected from a variety of species, sources and methods. These include data obtained from both experiment and computational simulation.
IMPC: the International Mouse Phenotyping Consortium (IMPC) is an international effort by 19 research institutions to identify the function of every protein-coding gene in the mouse genome. The entire genome of many species has now been published and whole genome sequencing is becoming relatively quick and cheap to complete. Despite these advancements the function of the majority of genes remains unknown.
elixir: ELIXIR unites Europe’s leading life science organisations in managing and safeguarding the increasing volume of data being generated by publicly funded research. It coordinates, integrates and sustains bioinformatics resources across its member states and enables users in academia and industry to access services that are vital for their research.
Global BioImaging Project: the imaging landscape changed significantly in the last 10 years as the the concept of open user access to cutting-edge technologies became valued and well recognized. In Europe imaging experts from 25 countries joined their forces and draw the vision of a pan-European imaging infrastructure, which gave momentum to the project of founding a Euro-BioImaging European Research Infrastructure Consortium (the EuBI ERIC).

Clinical Annotation

CIViC
DoCM
ClinVar
Intogen
Cancer Hotspots
DisGeNET
Cancer Biomarkers database
OncoKB: Precision Oncology Knowledge Base
LncRNADisease: Not only a resource that curated the experimentally supported lncRNA-disease association data but also a platform that integrated tool(s) for predicting novel lncRNA-disease associatons
fusiongdb: fusion gene annotation DataBase, which collected 48 117 FGs across pan-cancer from three representative fusion gene resources: the improved database of chimeric transcripts and RNA-seq data (ChiTaRS 3.1), an integrative resource for cancerassociated transcript fusions (TumorFusions), and The Cancer Genome Atlas (TCGA) fusions by Gao et al.
sedb: the comprehensive human Super-Enhancer database.
pmkb: the cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations
ewasdb: epigenome-wide association study database
dcdb: DCDB (Drug Combination Database), Accumulating scientific and clinical evidences have suggested the use of drug combinations as a safe and effective approach, to treat complicated and refractory diseases. The Drug Combination Database (DCDB) is devoted to the research and development of multi-component drugs. The current version of DCDB collected 1363 drug combinations (330 approved and 1033 investigational, including 237 unsuccessful usages), involving 904 individual drugs, 805 targets

Noncoding RNA Related Database

CSCD
AtCircDB
CircNet
circBase
circRNADb
exoRBase
EVLncRNAs
NONCODE: an integrated knowledge database dedicated to non-coding RNAs (excluding tRNAs and rRNAs)
MiTranscriptome: a catalog of human long poly-adenylated RNA transcripts derived from computational analysis of high-throughput RNA sequencing (RNA-Seq) data from over 6,500 samples spanning diverse cancer and tissue types
FANTOM CAT: an atlas of human long non-coding RNAs with accurate 5’ ends
lnc2cancer2: an updated database that provides comprehensive experimentally supported associations between lncRNAs and human cancers
sm2mir: a manual curated database which collects and incorporates the experimentally validated small molecules' effects on miRNA expression in 20 species from the published papers. Each entry contains the detailed information about small molecules, miRNAs and their relationships, including species, small molecule name, DrugBank Accession number, PubChem CID, approved by FDA or not, miRNA name, miRBase Accession number, expression pattern of miRNA, experimental detection method, tissues or conditions for detection, evidences in the reference, PubMed ID and the published year of the reference
oncomirdb: a Database for Oncogenic & Tumor-Suppressive MicroRNAs
mircancer: provides comprehensive collection of microRNA (miRNA) expression profiles in various human cancers which are automatically extracted from published literatures in PubMed. It utilizes text mining techniques for information collection. Manual revision is applied after auto-extraction to provide 100% precision
lncipedia: a public database for long non-coding RNA (lncRNA) sequence and annotation. The current release contains 127,802 transcripts and 56,946 genes
mirnest: an integrative collection of animal, plant and virus microRNA data
mirtarbase: the experimentally validated microRNA-target interactions database
mirdb: an online resource for microRNA target prediction and functional annotations

eQTL Related Database

exsnp
rVarBase
seeQTL
cancersplicingqtl: a database for genome-wide identification of splicing QTLs in human cancer

Sequencing Data Portal

Plant-related platforms

Plant Regulomics

Local tools

Quality Control

Alignment And Assembly

BWA
STAR
TMAP
NovoAlign
GMAP
bowtie
bowtie2
tophat2
hisat2
Edean
ABySS
SSAHA2
oases
Velvet
Trinity
MapSplice2
RUM
MECAT
DART
rHAT
taxmaps: large DNA/RNA metagenomics samples
MARVEL: consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.
vg: tools for working with genome variation graphs
TransLiG: a de novo transcriptome assembler that uses line graph iteration.
stringtie: Transcript assembly and quantification for RNA-Seq

Variant Detection (SNVs, INDELs, SVs)

GATK
MuTect
lofreq
VarScan2
freebayes
TVC
SomaticSniper
speedseq
FusionCatcher
svtoolkit
pindel
breakdancer
delly
CNVkit
speedseq
GRIDSS
PancanQTL
TumorFusions
SVScore
SVTools
RDDpred
iseq
deepvariant
SV2
facets
MutScan
svaba: structural variation and indel detection by local assembly
manta: structural variant and indel caller using mapped sequencing data
JAFFA: a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
Picky: structural variants pipeline for long reads
CREST: a algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data
Control-FREEC: a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data
Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs
GISTIC2: facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
BreaKmer: A method to identify structural variation from sequencing data in target regions
deTiN: DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
vadir: an integrated approach to Variant Detection in RNA
CN_Learn: a framework to integrate Copy Number Variant (CNV) predictions made by multiple algorithms using exome sequencing datasets
SVseq2
SoftSV: a tool for the detection of small and large deletions, inversions, tandem duplications and translocations from paired-end sequencing data.
wham: consists of two programs, wham and whamg. wham, the original tool, is a very sensitive method with a high false discovery rate. The second program, whamg, is more accurate and better suited for general structural variant (SV) discovery.

Variant Annotation

ANNOVAR
SnpEff
gemini
VEP
Variant Annotation Integrator
vcfanno
pcgr
annovarR
OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes
bystro: Bystro genetic analysis (annotation, filtering, statistics
contest: a tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data. Using a Bayesian framework, contamination levels are estimated from array based genotypes and sequencing reads
pathopredictor: Predict pathogenic and benign missense variant status.

Variant Visualization (SNVs, INDELs, SVs)

ProteinPaint
AGFusion
GenomeUPlot
BreakPointSurveyor
chimeraviz
Oncoprinter
MutationMapper
pv: 3D structure visualization in WEB
g2s: mappings between protein sequence positions and PDB 3D protein structure models
NGB: structural Variations (SVs) visualization capabilities, high performance, scalability, and cloud data support

Variant Screen

LARVA
DANN
NCBoost: Classifier of pathogenic non-coding variants in Mendelian diseases

Alternative Splicing

LeafCutter Annotation-free quantification of RNA splicing.
rMATS
MMSplice: variant effect predictions on splicing
pram predict intergenic transcript models from RNA-seq (Genome Res 2020)
shark Mapping-free filtering of irrelevant RNA-Seq reads（Bioinformatics 202）
PAIRADISE Paired Replicate Analysis of Allelic Differential Splicing Events (AJHG 2020)
IRFinder Detecting intron retention from RNA-Seq experiments
iread Detect intron retention(IR) events from RNA-seq datasets
DARTS Deep-learning Augmented RNA-seq analysis of Transcript Splicing
SpliceAI A deep learning-based tool to identify splice variants
DEXSeq Detecting differential usage of exons from RNA-seq data
MATS
cash Comprehensive alternative splicing hunting
tappas a comprehensive computational framework for the analysis of the functional impact of differential splicing
dsreg dSreg is a library to perform joint inference of differential splicing and regulatory mechanisms using RNA-seq data.
PSI-Sigma a comprehensive splicing detection method for short-read and long-read RNAseq analysis.
PsiCLASS Simultaneous multi-sample transcript assembler for RNA-seq data
IsoformSwitchAnalyzeR Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
yanagi Transcript Segment Library Construction for RNA-Seq Quantification
AStrap Identification of alternative splicing from transcript sequences without a reference genome
DSC A deep learning approach for classification of alternative splicing events
CATANA Comprehensive Alternative Transcripts Atlas based oN Annotation (CATANA) to identify all 10 known AS and AT events.
benchmarkingDiffExprAndSpl A benchmarking of workflows for detecting differential splicing and differential expression at isoform level in human RNA-seq studies
psichomics psichomics: graphical application for alternative splicing quantification and analysis
matt A Unix toolkit for analyzing genomic sequences with focus on down-stream analysis of alternative splicing events
PathwaySplice An R Package for Unbiased Splicing Pathway Analysis

Gene Expression Data Analysis

Cufflinks
DESeq2
edgeR
HTSeq
RESM: RNA-Seq by Expectation-Maximization, accurate quantification of gene and isoform expression from RNA-Seq data.
sRNAnalyzer
mrnn: an implementation of a Gated Recurrent Unit (GRU) network for classification of transcripts as either coding or noncoding
prada: pipeline for RNA-Sequencing Data Analysis
ballgown: a software package designed to facilitate flexible differential expression analysis of RNA-Seq data. It also provides functions to organize, visualize, and analyze the expression measurements for your transcriptome assembly.
subread: comprises a suite of software programs for processing next-gen sequencing read data, i.e. featureCounts: a software program developed for counting reads