Resources

Your comprehensive reference for bioinformatics tools, databases, and resources used in next-generation sequencing analysis. Each resource links to official documentation and relevant tutorials on NGS101.

Analysis Software & Tools

RNA-seq Analysis

Alignment & Quantification Tools

STAR (Spliced Transcripts Alignment to a Reference)

Ultra-fast RNA-seq aligner for splice-aware alignment
Official: STAR GitHub
Used in: RNA-seq Part 2: FASTQ to Counts

HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts)

Fast and sensitive alignment program for RNA-seq
Official: HISAT2 Site
Alternative to STAR with lower memory requirements

Salmon

Alignment-free transcript quantification tool
Official: Salmon Documentation
Fast pseudo-alignment alternative
Used in: RNA-seq Part 2: FASTQ to Counts

Kallisto

Ultra-fast transcript quantification from RNA-seq reads
Official: Kallisto Manual
Pseudo-alignment based quantification

featureCounts (from Subread package)

Highly efficient read summarization program
Official: Subread Package
Generates count matrices from BAM files
Used in: RNA-seq Part 2: FASTQ to Counts

HTSeq

Python framework for analyzing high-throughput sequencing data
Official: HTSeq Documentation
Alternative to featureCounts

Differential Expression Analysis

DESeq2

R package for differential gene expression analysis based on negative binomial distribution
Official: DESeq2 Bioconductor
Industry standard for RNA-seq DE analysis
Used in: RNA-seq Part 3: Count Table to DEGs
Compare with: limma vs DESeq2 vs edgeR Tutorial

limma-voom

Linear models for microarray and RNA-seq data with voom transformation
Official: limma Bioconductor
Excellent for complex experimental designs
Used in: Comparing DE Methods Tutorial

edgeR

Empirical analysis of digital gene expression data
Official: edgeR Bioconductor
Robust for low replicate counts
Used in: Comparing DE Methods Tutorial

Normalization Methods

TPM (Transcripts Per Million)

Within-sample normalization for gene length and library size
Used for: Gene expression comparison within samples
Learn more: RNA-seq Normalization Guide

RPKM/FPKM (Reads/Fragments Per Kilobase Million)

Traditional normalization for single-end/paired-end RNA-seq
Used for: Legacy comparison, avoid for DE analysis
Learn more: RNA-seq Normalization Guide

TMM (Trimmed Mean of M-values)

Between-sample normalization used by edgeR
Used for: Correcting sequencing depth and RNA composition
Learn more: RNA-seq Normalization Guide

Pathway & Functional Analysis

clusterProfiler

R package for GO, KEGG, and pathway enrichment analysis
Official: clusterProfiler Bioconductor
Comprehensive pathway analysis suite
Used in: RNA-seq Part 5: DEGs to Pathways

GSEA (Gene Set Enrichment Analysis)

Pathway analysis based on ranked gene lists
Official: GSEA Broad Institute
Gold standard for pathway analysis
Used in: RNA-seq Part 5: DEGs to Pathways

fgsea

Fast Gene Set Enrichment Analysis in R
Official: fgsea Bioconductor
Faster alternative to GSEA Java implementation

DAVID (Database for Annotation, Visualization and Integrated Discovery)

Web-based functional annotation tool
Official: DAVID Bioinformatics
User-friendly interface for beginners

Enrichr

Web-based gene list enrichment analysis tool
Official: Enrichr
Quick enrichment analysis with multiple databases

Network Analysis & Co-expression

WGCNA (Weighted Gene Co-expression Network Analysis)

R package for constructing gene co-expression networks
Official: WGCNA CRAN
Identifies gene modules and hub genes
Used in: WGCNA Tutorial

GENIE3

Gene regulatory network inference using random forests
Official: GENIE3 Bioconductor
Machine learning approach to network construction
Used in: GENIE3 Tutorial

RegEnrich

Master regulator analysis combining expression and regulatory networks
Official: RegEnrich Bioconductor
Identifies key transcription factors
Used in: Master Regulator Analysis Tutorial

RTN (Reconstruction of Transcriptional regulatory Networks)

R package for transcriptional network analysis
Official: RTN Bioconductor
Master regulator analysis
Used in: Master Regulator Analysis Tutorial

Clustering & Classification

Hierarchical Clustering

Standard clustering method in R (hclust, pheatmap)
Used for: Grouping samples or genes by expression patterns
Used in: Clustering Tutorial

K-means Clustering

Partition-based clustering algorithm
Used for: Identifying distinct gene expression clusters
Used in: Clustering Tutorial

PAM50

50-gene signature for breast cancer subtype classification
Official: genefu package
Clinical breast cancer classifier
Used in: Cancer Subtype Prediction

genefu

R package for gene expression-based classifiers
Official: genefu Bioconductor
Multiple cancer classifiers
Used in: Cancer Subtype Prediction

GSVA (Gene Set Variation Analysis)

Non-parametric, unsupervised method for gene set enrichment
Official: GSVA Bioconductor
Sample-level pathway activity scores
Used in: Cancer Subtype Prediction

Deconvolution & Cell Type Analysis

CIBERSORT

Estimate cell type proportions from bulk RNA-seq
Official: CIBERSORT Portal
Gold standard for immune cell deconvolution
Used in: Deconvolution Tutorial

EPIC (Estimating the Proportions of Immune and Cancer cells)

Deconvolution specialized for cancer samples
Official: EPIC GitHub
Estimates immune and cancer cell fractions
Used in: Deconvolution Tutorial

quanTIseq

Quantification of immune cell types from RNA-seq
Official: quanTIseq
Immune cell type quantification
Used in: Deconvolution Tutorial

Alternative Splicing Analysis

rMATS (Replicate Multivariate Analysis of Transcript Splicing)

Statistical detection of differential alternative splicing
Official: rMATS GitHub
Event-based splicing analysis
Used in: Alternative Splicing Tutorial

SUPPA2

Fast, accurate alternative splicing analysis
Official: SUPPA2 GitHub
Transcript-based splicing quantification
Used in: Alternative Splicing Tutorial

LeafCutter

Quantifies intron splicing ratios
Official: LeafCutter GitHub
Novel splice junction discovery
Used in: Alternative Splicing Tutorial

JunctionSeq

Differential usage of exons and splice junctions
Official: JunctionSeq Bioconductor
Visualizes differential splicing events

DEXSeq

Differential exon usage analysis
Official: DEXSeq Bioconductor
Identifies differential exon usage
Used in: Transcript-Level Splicing Tutorial

Isoform Analysis

StringTie

Transcript assembly and quantification
Official: StringTie
De novo transcript discovery
Used in: Isoform Analysis Tutorial

RSEM (RNA-Seq by Expectation-Maximization)

Accurate transcript quantification from RNA-seq
Official: RSEM GitHub
Handles multi-mapping reads
Used in: Isoform Analysis Tutorial

IsoformSwitchAnalyzeR

Identify isoform switches with functional consequences
Official: IsoformSwitchAnalyzeR Bioconductor
Predicts functional impact of isoform changes
Used in: Transcript-Level Splicing Tutorial

RNA Editing Analysis

REDItools

RNA editing detection from RNA-seq
Official: REDItools
A-to-I editing identification
Used in: RNA Editing Tutorial

JACUSA

Java framework for RNA editing detection
Official: JACUSA GitHub
Identifies RNA-DNA differences

SPRINT

SNP-free RNA editing identification
Official: SPRINT GitHub
Does not require DNA-seq data

Non-Coding RNA Analysis

CIRCexplorer2

Circular RNA identification from RNA-seq
Official: CIRCexplorer2 GitHub
circRNA detection and annotation
Used in: Circular RNA Tutorial

CIRI3

CircRNA identification tool
Official: CIRI GitHub
High sensitivity circRNA caller
Used in: Circular RNA Tutorial

CircRNA Databases

circBase: http://www.circbase.org/ (curated circRNA database)
circAtlas: http://circatlas.biols.ac.cn/ (tissue expression atlas)
circRNADb: http://reprod.njmu.edu.cn/circrnadb (functional annotations)
circInteractome: https://circinteractome.irp.nia.nih.gov/ (miRNA binding predictions)

miRDeep2

Discover known and novel miRNAs from small RNA-seq
Official: miRDeep2
miRNA discovery and quantification
Used in: miRNA-seq Tutorial

sRNAbench

Small RNA-seq analysis pipeline
Official: sRNAbench
Comprehensive small RNA profiling
Used in: Small RNA-seq Tutorial

UMI-tools

Handle Unique Molecular Identifiers in sequencing data
Official: UMI-tools GitHub
Deduplication with UMIs
Used in: UMI-Based miRNA-seq Tutorial

Structural Variation & Fusion Detection

STAR-Fusion

Fusion transcript detection from RNA-seq
Official: STAR-Fusion GitHub
Built on STAR aligner
Used in: Fusion Gene Tutorial

Arriba

Fast fusion detection from RNA-seq
Official: Arriba GitHub
Low false-positive rate
Used in: Fusion Gene Tutorial

FusionCatcher

Find somatic fusion genes, translocations and chimeras
Official: FusionCatcher
Specialized for cancer fusion detection
Used in: FusionCatcher Tutorial

Viral Sequence Detection

Kraken2

Taxonomic classification of metagenomic sequences
Official: Kraken2 GitHub
Fast viral detection
Used in: Viral Sequence Detection Tutorial

STAR + Viral Genome

Align to combined host and viral reference
Method: Map RNA-seq to host+viral genomes
Quantify viral gene expression
Used in: Viral Gene Expression Tutorial

Batch Effect & Covariates Correction

ComBat (from sva package)

Remove batch effects from expression data
Official: sva Bioconductor
Classic batch correction method
Used in: Batch Effects Tutorial

limma removeBatchEffect

Remove batch effects for visualization
Official: limma Bioconductor
Good for exploratory analysis
Used in: Batch Effects Tutorial

RUVSeq

Remove unwanted variation from RNA-seq
Official: RUVSeq Bioconductor
Uses negative control genes
Used in: Batch Effects Tutorial

Epigenetics Tools

ChIP-seq Analysis

HOMER (Hypergeometric Optimization of Motif EnRichment)

Complete ChIP-seq analysis suite
Official: HOMER
Peak calling, motif discovery, annotation
Used in: ChIP-seq Part 1: FASTQ to Peaks with HOMER

MACS2 (Model-based Analysis of ChIP-Seq)

Peak caller for ChIP-seq data
Official: MACS GitHub
Industry standard peak caller
Used in: ChIP-seq Part 4: FASTQ to Peaks with MACS2

DiffBind

Differential binding analysis for ChIP-seq/ATAC-seq
Official: DiffBind Bioconductor
Consensus peak analysis
Used in: ChIP-seq Part 3: Differential Binding, ATAC-seq Part 2: DiffBind

IDR (Irreproducible Discovery Rate)

Assess reproducibility between ChIP-seq replicates
Official: IDR GitHub
Quality control for replicates
Used in: ChIP-seq Part 5: IDR Analysis

deepTools

Suite for ChIP-seq data visualization and QC
Official: deepTools
Heatmaps, profile plots, correlation
Used in: ChIP-seq Part 2: Visualization

ChIPseeker

R package for ChIP peak annotation and visualization
Official: ChIPseeker Bioconductor
Annotate peaks to nearest genes
Used in: ChIP-seq Part 3: Differential Binding

MEME Suite

Motif discovery and analysis tools
Official: MEME Suite
Comprehensive motif analysis
Used in: ChIP-seq Part 3: Differential Binding

ATAC-seq Analysis

MACS2 (for ATAC-seq)

Peak calling optimized for ATAC-seq
Official: MACS GitHub
Use with –shift parameters for ATAC
Used in: ATAC-seq Part 1: FASTQ to Peaks

Genrich

Peak caller designed for ATAC-seq and ChIP-seq
Official: Genrich GitHub
Handles replicates effectively
Used in: ATAC-seq Part 1: FASTQ to Peaks

TOBIAS (Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal)

Transcription factor footprinting from ATAC-seq
Official: TOBIAS
Differential footprinting analysis
Used in: ATAC-seq Part 3: Footprinting

HINT-ATAC

Footprinting tool for ATAC-seq
Official: RGT Suite
TF binding site prediction
Used in: ATAC-seq Part 3: Footprinting

ArchR

R package for ATAC-seq and single-cell ATAC-seq
Official: ArchR
Comprehensive ATAC-seq analysis
Used in: ATAC-seq and RNA-seq Integration

CUT&RUN/CUT&Tag Analysis

SEACR (Sparse Enrichment Analysis for CUT&RUN)

Peak caller specialized for CUT&RUN data
Official: SEACR GitHub
Works without input controls
Used in: CUT&RUN/Tag Tutorial

MACS2 (for CUT&RUN)

Can be adapted for CUT&RUN analysis
Official: MACS GitHub
Use with adjusted parameters
Alternative in: CUT&RUN/Tag Tutorial

Hi-C & 3D Genome Organization

Juicer

Complete Hi-C analysis pipeline
Official: Juicer
From raw reads to contact maps
Used in: Hi-C Tutorial

HiC-Pro

Optimized and flexible Hi-C processing pipeline
Official: HiC-Pro
Fast Hi-C data processing

cooler

Store and access sparse contact matrices
Official: cooler GitHub
Efficient Hi-C data storage

Juicebox

Visualization software for Hi-C data
Official: Juicebox
Interactive contact map viewer
Used in: Hi-C Tutorial

DNA Methylation Analysis

minfi

Illumina methylation array analysis in R
Official: minfi Bioconductor
EPIC and 450k array analysis
Used in: DNA Methylation Part 1: EPIC Arrays

ChAMP

Chip Analysis Methylation Pipeline
Official: ChAMP Bioconductor
Comprehensive array analysis
Used in: DNA Methylation Part 1: EPIC Arrays

Bismark

Bisulfite read mapper and methylation caller
Official: Bismark
Gold standard for WGBS/RRBS
Used in: DNA Methylation Part 2: WGBS/RRBS

methylKit

R package for DNA methylation analysis
Official: methylKit Bioconductor
Differential methylation analysis
Used in: DNA Methylation Part 3: Biological Insights

DSS (Dispersion Shrinkage for Sequencing data)

Differential methylation for bisulfite sequencing
Official: DSS Bioconductor
Robust statistical testing
Used in: DNA Methylation Part 3: Biological Insights

Genomics & Variant Analysis

Alignment Tools

BWA (Burrows-Wheeler Aligner)

Fast and accurate DNA sequence aligner
Official: BWA
Standard for WGS/WES alignment
Used in: WGS Part 1: Raw Reads to Variants

Bowtie2

Fast and memory-efficient read aligner
Official: Bowtie2
Good for longer reads
Alternative for WGS alignment

minimap2

Versatile aligner for long reads and assemblies
Official: minimap2
Excellent for Oxford Nanopore and PacBio

Variant Calling – Germline

GATK (Genome Analysis Toolkit)

Industry standard for germline variant calling
Official: GATK Broad Institute
HaplotypeCaller for germline variants
Used in: WGS Part 1: Raw Reads to Variants, WES Tutorial

FreeBayes

Bayesian genetic variant detector
Official: FreeBayes
Haplotype-based variant detection

DeepVariant

Deep learning-based variant caller
Official: DeepVariant
High accuracy with deep neural networks

Variant Calling – Somatic

Mutect2 (GATK)

Somatic mutation caller for tumor-normal pairs
Official: GATK Mutect2
Gold standard for somatic variant calling
Used in: WGS Part 2A: Tumor-Normal Mutation Calling

VarScan2

Variant detection for massively parallel sequencing
Official: VarScan
Somatic and germline calling
Used in: WGS Part 2B: Unmatched Sample Strategies

MuSE

Somatic mutation caller for tumor-normal pairs
Official: MuSE
Good for tumor purity estimation
Used in: WGS Part 2B: Unmatched Sample Strategies

SomaticSniper

Identify somatic mutations in tumor/normal pairs
Official: SomaticSniper
Fast SNV calling

Variant Annotation

ANNOVAR

Functional annotation of genetic variants
Official: ANNOVAR
Comprehensive variant annotation
Used in: WGS Part 3: Annotating Variants

VEP (Variant Effect Predictor)

Ensembl’s variant annotation tool
Official: VEP
Rich functional annotations
Used in: WGS Part 3: Annotating Variants

SnpEff

Genomic variant annotation and effect prediction
Official: SnpEff
Fast functional annotation
Used in: WGS Part 3: Annotating Variants

InterVar

Clinical interpretation of variants
Official: InterVar
ACMG guideline-based classification
Used in: WGS Part 5: Disease-Specific Variants

Copy Number Variation (CNV)

CNVkit

Copy number variation detection from targeted sequencing
Official: CNVkit
Tumor CNV calling
Used in: WGS Part 6-2: Tumor CNVs, WES Tutorial

GATK gCNV

Germline CNV calling pipeline
Official: GATK gCNV
Reference-based CNV detection
Used in: WGS Part 6: Germline CNVs

XHMM

Exome-based CNV detection
Official: XHMM
Specialized for exome data
Used in: WGS Part 6: Germline CNVs

GISTIC2

Identify significant copy number alterations in cancer
Official: GISTIC2
Tumor CNV significance analysis

Mutation Visualization & Interpretation

maftools

Summarize, visualize and analyze MAF files
Official: maftools Bioconductor
Comprehensive mutation analysis
Used in: WGS Part 4: Visualizing Mutations

MutationalPatterns

Extract and visualize mutational signatures
Official: MutationalPatterns Bioconductor
COSMIC signature analysis
Used in: WGS Part 4: Visualizing Mutations

deconstructSigs

Identify mutational signatures in tumor samples
Official: deconstructSigs
Signature decomposition
Used in: WGS Part 4: Visualizing Mutations

GWAS & Population Genetics

PLINK

Whole genome association analysis toolset
Official: PLINK
Standard for GWAS analysis
Used in: GWAS Tutorial

GCTA

Genome-wide complex trait analysis
Official: GCTA
Heritability estimation

LocusZoom

Regional association plot visualization
Official: LocusZoom
GWAS results visualization

Single-Cell Analysis

scRNA-seq Analysis

CellRanger (10x Genomics)

Process 10x Chromium single-cell data
Official: CellRanger
From FASTQ to count matrix
Used in: scRNA-seq Part 1: FASTQ to Count Matrix

STARsolo

Single-cell RNA-seq alignment and quantification
Official: STAR GitHub
Alternative to CellRanger
Used in: scRNA-seq Part 1: FASTQ to Count Matrix

Seurat

R toolkit for single-cell genomics
Official: Seurat
Industry standard for scRNA-seq analysis
Used in: scRNA-seq Part 2: QC, Part 3: Integration, Part 4: Cell Type ID

Scanpy

Python-based single-cell analysis
Official: Scanpy
Scalable single-cell analysis

SingleCellExperiment

Bioconductor infrastructure for single-cell data
Official: SingleCellExperiment
Data structure for scRNA-seq

scRNA-seq Quality Control

DoubletFinder

Detect doublets in single-cell RNA-seq
Official: DoubletFinder
Doublet detection
Used in: scRNA-seq Part 2: QC

Scrublet

Python package for doublet detection
Official: Scrublet
Simulation-based doublet detection

miQC

Flexible quality control for scRNA-seq
Official: miQC Bioconductor
Model-based QC

scRNA-seq Integration & Batch Correction

Harmony

Fast integration of single-cell data
Official: Harmony
Scalable batch correction
Used in: scRNA-seq Part 3: Integration

Seurat Integration

Canonical correlation analysis-based integration
Official: Seurat Integration
Built into Seurat workflow
Used in: scRNA-seq Part 3: Integration

scVI (single-cell Variational Inference)

Deep learning for scRNA-seq analysis
Official: scVI
Neural network-based integration

Cell Type Annotation

SingleR

Automated cell type annotation
Official: SingleR Bioconductor
Reference-based annotation
Used in: scRNA-seq Part 4: Cell Type ID

CellTypist

Machine learning-based cell type classifier
Official: CellTypist
Pre-trained models for annotation

Azimuth

Reference-based cell type mapping
Official: Azimuth
Web-based and R package

Quality Control & Utilities

Sequencing Quality Control

FastQC

Quality control tool for high throughput sequence data
Official: FastQC
First-pass quality assessment
Used across all NGS tutorials

MultiQC

Aggregate results from multiple bioinformatics analyses
Official: MultiQC
Comprehensive QC reporting
Used across all NGS tutorials

Trimmomatic

Flexible read trimming tool for Illumina data
Official: Trimmomatic
Adapter trimming and quality filtering

Cutadapt

Finds and removes adapter sequences
Official: Cutadapt
Flexible adapter removal

fastp

Ultra-fast FASTQ preprocessing
Official: fastp
All-in-one FASTQ processor

File Manipulation & Utilities

SAMtools

Suite for manipulating alignments in SAM/BAM format
Official: SAMtools
Essential for BAM file operations
Used across all NGS tutorials

BEDtools

Toolset for genome arithmetic
Official: BEDtools
Interval operations on genomic features
Used across multiple tutorials

BCFtools

Utilities for variant calling and manipulating VCF/BCF files
Official: BCFtools
VCF file manipulation

Picard

Java-based tools for manipulating HTS data
Official: Picard
Mark duplicates, collect metrics
Used in: WGS Part 1

IGV (Integrative Genomics Viewer)

Visualization tool for genomics data
Official: IGV
Interactive genome browser
Used for visualization across tutorials

UCSC Genome Browser

Web-based genome browser
Official: UCSC Browser
Explore genomic data

R Visualization Packages

ggplot2

Data visualization package for R
Official: ggplot2
Publication-quality plots
Used in: RNA-seq Part 4: Publication Figures

pheatmap

Pretty heatmaps in R
Official: pheatmap
Heatmap generation
Used across RNA-seq tutorials

ComplexHeatmap

Make complex heatmaps in R
Official: ComplexHeatmap Bioconductor
Advanced heatmap visualization

EnhancedVolcano

Publication-ready volcano plots
Official: EnhancedVolcano Bioconductor
Volcano plot customization
Used in: RNA-seq Part 4: Publication Figures

CRISPR Screen Analysis

MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout)

Identify essential genes from CRISPR screens
Official: MAGeCK
sgRNA library analysis
Used in: CRISPR Screen Tutorial

CRISPResso2

Analysis of CRISPR editing outcomes
Official: CRISPResso2
Editing efficiency quantification

Databases & Data Resources

Gene Expression Databases

NCBI GEO (Gene Expression Omnibus)

Public repository for gene expression data
Official: GEO
Download published datasets
Used in: Submitting to GEO Tutorial

TCGA (The Cancer Genome Atlas)

Comprehensive cancer genomics data
Official: TCGA via GDC
33 cancer types, multi-omics
Used in: TCGA Data Download Tutorial

GTEx (Genotype-Tissue Expression)

Gene expression across human tissues
Official: GTEx Portal
Normal tissue expression reference
Used in: GTEx Data Download Tutorial

ArrayExpress

Functional genomics data archive
Official: ArrayExpress
European alternative to GEO

recount3

Unified access to RNA-seq datasets
Official: recount3
Pre-processed RNA-seq data

GEPIA3 (https://gepia3.bioinfoliu.com/) – Gene Expression Profiling Interactive Analysis v3

Interactive web tool for analyzing RNA-seq data from TCGA and GTEx
Focused on cancer genomics and differential expression analysis

UCSC Xena (https://xena.ucsc.edu/) – UCSC Xena Browser

Multi-omic data visualization platform
Hosts TCGA, GTEx, and other large cancer genomics datasets

Reference Genomes & Annotations

GENCODE

High-quality gene annotations
Official: GENCODE
Human and mouse annotations
Used across all RNA-seq tutorials

Ensembl

Genome browser and annotation database
Official: Ensembl
Comprehensive genome annotations
Used across tutorials

UCSC Genome Browser

Reference genomes and annotations
Official: UCSC Downloads
Alternative genome references

RefSeq

NCBI Reference Sequence Database
Official: RefSeq
Curated gene annotations

refgenie

Reference genome manager
Official: refgenie
Pre-built genome references

Illumina iGenomes

Ready-to-use reference sequences and annotations
Official: iGenomes
Pre-indexed genomes

Variant & Population Databases

gnomAD (Genome Aggregation Database)

Population allele frequencies
Official: gnomAD
140,000+ genomes/exomes
Used in: WGS Part 5: Disease Variants

ClinVar

Variation-disease relationships
Official: ClinVar
Clinical variant interpretation
Used in: WGS Part 5: Disease Variants

dbSNP

Short genetic variations
Official: dbSNP
Variant IDs and frequencies

1000 Genomes

Human genetic variation catalog
Official: 1000 Genomes
Population genetics reference

COSMIC (Catalogue of Somatic Mutations in Cancer)

Cancer somatic mutation database
Official: COSMIC
Cancer mutation catalog

Database of Genomic Variants (DGV)

Structural variation in healthy individuals
Official: DGV
Benign CNV reference

Clinical & Disease Databases

OMIM (Online Mendelian Inheritance in Man)

Human genes and genetic disorders
Official: OMIM
Gene-disease relationships

ClinGen

Clinical genome resource
Official: ClinGen
Gene-disease validity

DECIPHER

Database of genomic variation and phenotype
Official: DECIPHER
Rare disease genomics

GenCC (Gene Curation Coalition)

Curated gene-disease relationships
Official: GenCC
Standardized gene-disease assertions

HGMD (Human Gene Mutation Database)

Disease-causing mutations
Official: HGMD
Mutation catalog (subscription)

Orphanet

Rare disease and orphan drug portal
Official: Orphanet
Rare disease information

cBioPortal

Cancer genomics data visualization
Official: cBioPortal
Interactive cancer genomics
Used in mutation visualization

Pathway & Functional Databases

MSigDB (Molecular Signatures Database)

Gene sets for pathway analysis
Official: MSigDB
Hallmark, GO, KEGG gene sets
Used in: RNA-seq Part 5: Pathways

KEGG (Kyoto Encyclopedia of Genes and Genomes)

Pathway and disease databases
Official: KEGG
Metabolic and signaling pathways

Reactome

Pathway knowledge base
Official: Reactome
Curated pathway database

Gene Ontology (GO)

Gene function classification
Official: GO
Biological process, molecular function, cellular component

WikiPathways

Community-curated pathway database
Official: WikiPathways
Open-source pathways

Regulatory & Epigenetics Databases

ENCODE

Encyclopedia of DNA Elements
Official: ENCODE
Functional genomics data
ChIP-seq, ATAC-seq, RNA-seq datasets

TRRUST (Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining)

Human/mouse transcription factor-target interactions
Official: TRRUST
TF regulatory networks
Used in network analysis tutorials

RegNetwork

Regulatory network repository
Official: RegNetwork
TF-target gene relationships

JASPAR

Transcription factor binding profile database
Official: JASPAR
TF motifs

Cistrome DB

ChIP-seq and chromatin accessibility database
Official: Cistrome DB
Curated ChIP-seq data

miRNA Databases

miRBase

MicroRNA sequences and annotation
Official: miRBase
miRNA reference database
Used in: miRNA-seq tutorials

TargetScan

Predict miRNA target sites
Official: TargetScan
miRNA-mRNA interactions

miRDB

MicroRNA target prediction database
Official: miRDB
miRNA target genes

Single-Cell Reference Databases

Human Cell Atlas

Reference maps of human cells
Official: Human Cell Atlas
Single-cell reference data

PanglaoDB

Single-cell sequencing database
Official: PanglaoDB
Cell type markers

CellMarker

Cell marker database
Official: CellMarker
Manually curated cell markers

Computing & Environment

Package Management

Conda / Miniforge

Package and environment manager
Official: Miniforge
Python and R package installation
Used in: RNA-seq Part 1: Environment Setup

Bioconda

Bioinformatics software distribution
Official: Bioconda
9000+ bioinformatics packages
Browse: Bioconda Package Index

Conda-forge

Community-driven conda channel
Official: Conda-forge
General software packages
Browse: Conda-forge Packages

Programming Languages & IDEs

Statistical computing language
Official: R Project
Essential for bioinformatics analysis
Used across all tutorials

RStudio

Integrated development environment for R
Official: RStudio
User-friendly R interface

Python

General-purpose programming language
Official: Python
Versatile for bioinformatics

Jupyter

Interactive computing notebooks
Official: Jupyter
Python/R notebook interface

High Performance Computing (HPC)

Slurm

Workload manager for HPC clusters
Official: Slurm
Job submission and management
Used in: Slurm Tutorial

PBS/Torque

Alternative HPC job scheduler
Official: PBS Works
Cluster job management

SGE (Sun Grid Engine)

Distributed resource management
Alternative HPC scheduler

Containerization

Docker

Platform for developing and running applications in containers
Official: Docker
Reproducible analysis environments
Used in: Docker Tutorial

Singularity/Apptainer

Container platform for HPC
Official: Apptainer
HPC-friendly containerization

Workflow Management

Snakemake

Workflow management system for Python
Official: Snakemake
Reproducible and scalable analysis

Nextflow

Data-driven computational pipelines
Official: Nextflow
Portable workflow framework

WDL (Workflow Description Language)

Workflow specification language
Official: WDL
Used by GATK pipelines

Learning Resources

Cheat Sheets

Conda Cheat Sheet

Quick reference for conda commands
Official: Conda Cheat Sheet

R Cheat Sheets (Posit)

Comprehensive R package cheat sheets
Official: Posit Cheat Sheets
ggplot2, dplyr, tidyr, and more

R Cheat Sheets (Kaggle)

Community R cheat sheet collection
Community: Kaggle R Cheat Sheets

data.table Cheat Sheet

Fast data manipulation in R
Official: data.table Cheat Sheet

ggplot2 Cheat Sheet

Data visualization with ggplot2
Official: ggplot2 Cheat Sheet

Unix Command Line Cheat Sheet

Essential Linux/Unix commands
Various resources available online

Documentation Hubs

Bioconductor

R packages for genomic data analysis
Official: Bioconductor
2000+ bioinformatics packages

Galaxy Project

Web-based platform for data analysis
Official: Galaxy
No-code bioinformatics

NGS 101 Complete Tutorial Library

Your current site – 70+ comprehensive tutorials
Home: NGS 101 Tutorials
Beginner-friendly, step-by-step guides

Quick Reference

File Formats Guide

FASTQ Format

Raw sequencing reads with quality scores
Learn: NGS Data Types Guide

BAM/SAM Format

Sequence Alignment/Map format
Learn: NGS Data Types Guide

VCF/BCF Format

Variant Call Format
Learn: NGS Data Types Guide

BED Format

Browser Extensible Data format
Learn: NGS Data Types Guide

GTF/GFF Format

Gene Transfer/General Feature Format
Learn: NGS Data Types Guide

Complete File Format Reference

Comprehensive guide to all NGS file types
Tutorial: NGS Data Types and Formats

Data Management

HPC Data Management Guide

Storage, transfer, and sharing best practices
Tutorial: HPC Data Management

NCBI Database Guide

Complete guide to NCBI resources
Tutorial: NCBI Databases

Additional Resources

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Website: BullishBooks.com
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This resource page is continuously updated as new tools and tutorials are added. Last update: January 2026

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Tags:

RNA-seq analysis tools, ChIP-seq software, ATAC-seq analysis, DNA methylation tools, variant calling pipelines, single-cell RNA-seq, bioinformatics databases, genomics tools, NGS data analysis, DESeq2 tutorial, GATK variant calling, Seurat single-cell, WGCNA network analysis, pathway enrichment tools, cancer genomics databases, TCGA data access, GEO database, reference genomes, bioconductor packages, conda bioinformatics, HPC cluster computing, Docker containerization, variant annotation, copy number analysis, fusion gene detection, alternative splicing analysis, epigenetics tools, Hi-C analysis, CRISPR screen analysis, GWAS tools, population genetics databases, clinical variant interpretation, transcription factor databases, miRNA target prediction, cell type deconvolution, batch effect correction, quality control tools, genome visualization, mutation signature analysis.