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scRNA-seq_notes
A list of scRNA-seq analysis toolsHiC_tools
A collection of tools for Hi-C data analysisMachineLearning_notes
Machine learning and deep learning resourcesHiC_data
A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.TCGAsurvival
Scripts to analyze TCGA dataCancer_notes
A continually expanding collection of cancer genomics notes and dataStatistics_notes
Statistics, data analysis tutorials and learning resourcesscATAC-seq_notes
scATAC-seq data analysis tools and papersImmuno_notes
Immunology-related bioinformatics data and toolsscHiC_notes
Notes on single-cell Hi-C technologies, tools, and dataMDnotes
Links to all data science, genomics, and other notesRNA-seq_notes
A continually expanding collection of RNA-seq toolsBrain_genomic_data
Brain-related -omics dataSNP_notes
Notes on SNP-related tools and genome variation analysisgwas2bed
Extracting disease-specific genomic coordinates from GWAS catalogChIP-seq_notes
Notes on ChIP-seq and other-seq-related toolsblogs
Links to data science, bioinformatics, statistics, and machine learning resourcesAging
Epigenomic enrichment analysis of age-related genomic regionsMicrobiome_notes
A continually expanding collection of microbiome analysis toolsRNA-seq
RNA-seq analysis scriptsAging_clock
Data and papers related to epigenetic clocks predicting ageHiCcompareWorkshop
Differential Hi-C Data Analysis Workshop https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.76genomerunner_web
Web version of GenomeRunnerR_notes
Data science in R notesProgramming_notes
Programming-related notesMethylation_notes
Notes on DNA methylation analysisbioinformatics-impact
GitHub statistics as a measure of the impact of open-source bioinformatics softwareE-MTAB-3610
Processed E-MTAB-3610 dataset - Transcriptional Profiling of 1,000 human cancer cell linesBIOS668.2018
Web site for "Statistical Methods for High-throughput Genomic Data II" BIOS 668 course, Spring 2018 https://mdozmorov.github.io/BIOS668.2018presentations
Talks and related materialPython_notes
Data science in Python notesmanuscript_template
Template of a manuscript in RmdJobs_notes
Notes for job seekerspromoter_extract
Extract genomic coordinates of the promoters from a list of genes.ChIP-seq
Scripts to analyze ChIP-seq dataBIOS691_Cancer_Bioinformatics
Course material for the BIOS691 "Cancer Bioinformatics" course, January 25 - May 7, 2021Talk_3Dgenome
Slides for "The genome in action: Detecting and interpreting changes in the 3D genome organization" talkCTCF
Genomic coordinates of FIMO-predicted CTCF binding sites using JASPAR and other PWMs, human and mouse genome assemblies including mm39 and T2T. Also included experimentally derived ENCODE SCREEN CTCF-bound CREs.MDgenomerunner
MD functions mostly for GenomeRunner project. See MDmisc R package for MD miscellaneous functionsbios524-r-2021
"Biostatistical Computing with R" courseBIOS691_deep_learning_R
"Deep Learning with R" course materialHMP2
16S rRNA sequencing data for the HMP2 projectTalk_reproducible_research_overview_2021
Brief overview of computational reproducible research, Unix, remote computing (SSH), Conda, pipelines, R/RMarkdown, Git/GitHub, Docker, Cloud, Kubernetes. The goal is to provide students with modern data science ecosystem of tools for further studies.MDmisc
MD helper functions. Previous version at https://github.com/mdozmorov/MDgenomerunnerR.genomerunner
Scripts and examples of visualization and analysis of the enrichment and epigenomic similarity resultsdcaf
Misc. scripts and examplesGrants_notes
Notes on potential funding opportunitiesactiveranges
Expanding collection of biologically active chromatin regions as GRanges.GTEx
Playground with GTEx data63_immune_cells
Gene expression profiles of 63 immune cell typesR.Lorin.RNA-seq
Interpretation of RNA-seq dataTalk_preciseTAD
Slides for "preciseTAD: A transfer learning framework for 3D domain boundary prediction at base-pair resolution" presentationGenomeRunner
Automating genome explorationTalk_Genomics
Talk for the Science Club, Department of Pathology, VCU. May 15, 2019.PCAworkshop
A introduction to PCA in Rdeconvolution
Cell type-specific deconvolution of 'omics' dataTalk_JSM2019
Slides for JSM2019, "SpectralTAD: Defining Hierarchy of Topologically Associated Domains Using Graph Theoretical Clustering"Methylation850K
Methylation analysis of Illumina 850K arraysbeamer_template
Beamer template for RMarkdown class presentationTalk_ISMB2020
TADcompare abstract for the virtual ISMB 2020 conferencegrdocs
GenomeRunner documentationR.-ChIP-seq.histone
Analysis of histone marks, and their differential presence in the genomeTalk_HiCcompare
Slides for HiCcompareWorkshopR.Sjogren
Sjogren syndrome microarray data analysislecture1
Test repoBIOS567
Web site for "Statistical Methods for High-throughput Genomic Data I" BIOS 567 coursePathwayRunner
PathwayRunner computed enrichment of gene set(s) in all pathways using hypergeometric testGDS-processor
Process GDS files from Gene Expression Omnibus (GEO)Talk_Hi-C
An overview presentation of chromatin conformation capture technologies and analysis methods.Quantile-normalization
Quantile normalization of gene expression matrix with missing valuesRepeatSoaker
a simple method to eliminate low-complexity short readsBIOS567.2017
Web site for "Statistical Methods for High-throughput Genomic Data I" BIOS 567 course, Fall 2017Love Open Source and this site? Check out how you can help us