Pipelines

• A collection of high quality Nextflow pipelines

For Heatmap

• iheatmapR

Co-expression network analysis

• CEMiTool

• WGCNA

• LINC

• lionessR

Analyzing Mass spectrometry Data

• Mass Spectrometry Data Analysis with Spectra

Networks

• STRING: functional protein association networks

• Markov Clustering

Gene-fusion detection

• Clinker

• Tools capable of detecting fusion genes

• FuSeq

Transcription factor prediction

• BART

ATAC-Seq

• ATAC-seq data analysis: from FASTQ to peaks
• From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis

Flow cytometry

• CyTOF - Differential analysis of High-dimensional mass and flow cytometry

DNA-methylation

• DNA-methylation Analysis
• Analysis of 450k DNA methylation data with minfi
• decorate: Differential Epigenetic Correlation Test

Structural Variant Caller

• Strelka2: fast and accurate calling of germline and somatic variants

Geneset Enrichment Analysis

• DESeq results to pathways with the fgsea package
• gerr: Gene set enrichment with regularized regression

Mutational Signature Analysis

• MuSiCa - Web app
• Helmsman: fast and efficient mutation signature analysis for massive sequencing datasets
• SMuRF: Portable and accurate ensemble prediction of somatic mutations

Single Cell RNA-Seq Analysis

• A workflow for single cell RNA-seq data analysis
• A SingleCell RNASeq pre-processing snakemake workflow

Super Enhancer Analysis

• SEanalysis: a web tool for super-enhancer associated regulatory analysis

Integrating Data

• Integrating ChIP-seq with other functional genomics data

Cancer Datasets portals and related R packages

• TCGA Legacy Archive

• TCGA Harmonized

• Human Protein Atlas

• International Cancer Genome Consortium (ICGC)

• cBioportal

• TCGAbiolinks

• GenomicDataCommons

• RTCGA

• FireBrowse

• Xena Browser

• PAN Cancer Data GDC

• Cancer Cell Line Encyclopedia

Different Tools and R packages

• svist4get: a simple visualization tool for genomic tracks from sequencing experiments
• DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis
• CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models
• Cancermine: Text-mined knowledgebase for drivers, oncogenes and tumor suppressors in cancer
• DeepLncRNA: Prediction of LncRNA Subcellular Localization with Deep Learning from Sequence Features
• trackViewer: a Bioconductor package for interactive and integrative visualization of multi-omics data
• [pVACtools: a computational toolkit to identify and visualize cancer neoantigens]
• RNASeqR : RNA-Seq analysis based on one independent variable
• LncADeep: An ab initio lncRNA identification and functional annotation tool based on deep learning
• circDeep: Deep learning approach for circular RNA classification from other long non-coding RNA
• PDF Scraping in R with tabulizer
• How to extract tabular data from PDFs with R
• The magick package: Advanced Image-Processing in R
• Best practices for bioinformatic characterization of neoantigens for clinical utility
• ViSEAGO:Visualisation, Semantic similarity, Enrichment Analysis of Gene Ontology.
• SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
• caOmicsV: an R package for visualizingmultidimensional cancer genomic data
• [GDCRNAtools]((https://academic.oup.com/bioinformatics/article/34/14/2515/4917355)

Deep Learning in Bioinformatics

• janggu

Personal site designing on Github

• github.io creation