mdozmorov/SNP_notes

Notes on SNP-related tools and genome variation analysis

Size: 1.09 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 28 - Forks: 11

mdozmorov/HiC_tools

A collection of tools for Hi-C data analysis

Size: 2.94 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 597 - Forks: 134

mdozmorov/Cancer_notes

A continually expanding collection of cancer genomics notes and data

Size: 73.7 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 107 - Forks: 33

mdozmorov/GitHub_metrics

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mdozmorov/RNA-seq

RNA-seq analysis scripts

Language: Shell - Size: 2.62 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 15 - Forks: 6

mdozmorov/scRNA-seq_notes

A list of scRNA-seq analysis tools

Language: R - Size: 2.46 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 709 - Forks: 160

mdozmorov/Aging_clock

Data and papers related to epigenetic clocks predicting age

Language: R - Size: 3.62 MB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 28 - Forks: 4

mdozmorov/CTCF

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.

Language: R - Size: 1.55 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 7 - Forks: 1

mdozmorov/MDnotes

Links to all data science, genomics, and other notes

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mdozmorov/BIOS658_2025

BIOS 658. Statistical Methods for High-throughput Genomics Data I

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mdozmorov/MachineLearning_notes

Machine learning and deep learning resources

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mdozmorov/Grants_notes

Notes on potential funding opportunities

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mdozmorov/Methylation_notes

Notes on DNA methylation analysis

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mdozmorov/BIOS691_deep_learning_R_2025

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mdozmorov/R_notes

Data science in R notes

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mdozmorov/Bioinformatics_notes

Bioinformatics and genomics resources

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mdozmorov/TCGAsurvival

Scripts to analyze TCGA data

Language: R - Size: 14.6 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 120 - Forks: 45

mdozmorov/Statistics_notes

Statistics, data analysis tutorials and learning resources

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mdozmorov/HiC_data

A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

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mdozmorov/scATAC-seq_notes

scATAC-seq data analysis tools and papers

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mdozmorov/RNA-seq_notes

A continually expanding collection of RNA-seq tools

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mdozmorov/Python_notes

Data science in Python notes

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mdozmorov/Programming_notes

Programming-related notes

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mdozmorov/scHiC_notes

Notes on single-cell Hi-C technologies, tools, and data

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mdozmorov/MDtemplate

A template for coding in RMarkdown

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mdozmorov/ChIP-seq_notes

Notes on ChIP-seq and other-seq-related tools

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mdozmorov/gbcc2025 Fork of Bioconductor/gbcc2025

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mdozmorov/Immuno_notes

Immunology-related bioinformatics data and tools

Size: 14.5 MB - Last synced at: 5 months ago - Pushed at: about 1 year ago - Stars: 71 - Forks: 34

mdozmorov/Data_notes

Lists of publicly available datasets for machine learning

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mdozmorov/bioinformatics-impact

GitHub statistics as a measure of the impact of open-source bioinformatics software

Language: TeX - Size: 2.15 MB - Last synced at: 6 days ago - Pushed at: about 2 years ago - Stars: 9 - Forks: 1

mdozmorov/Brain_genomic_data

Brain-related -omics data

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mdozmorov/Microbiome_notes

A continually expanding collection of microbiome analysis tools

Size: 40 KB - Last synced at: 5 months ago - Pushed at: over 3 years ago - Stars: 17 - Forks: 2

mdozmorov/E-MTAB-3610

Processed E-MTAB-3610 dataset - Transcriptional Profiling of 1,000 human cancer cell lines

Language: R - Size: 31.2 MB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 11 - Forks: 0

mdozmorov/Talk_VCU_Physiology_2024-10-24

"3D genomics of drug resistance in breast cancer" presentation in the Department of Physiology, VCU

Language: SCSS - Size: 22.5 MB - Last synced at: 5 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

mdozmorov/Jobs_notes

Notes for job seekers

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mdozmorov/Conference_notes

Notes on potential conferences

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mdozmorov/HiCcompareWorkshop

Differential Hi-C Data Analysis Workshop https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.76

Language: Dockerfile - Size: 5.12 MB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 15 - Forks: 5

mdozmorov/R.-ChIP-seq.histone

Analysis of histone marks, and their differential presence in the genome

Language: R - Size: 145 KB - Last synced at: 5 months ago - Pushed at: over 11 years ago - Stars: 2 - Forks: 0

mdozmorov/promoter_extract

Extract genomic coordinates of the promoters from a list of genes.

Language: Python - Size: 441 KB - Last synced at: about 2 months ago - Pushed at: about 10 years ago - Stars: 5 - Forks: 0

mdozmorov/Breast_cancer

Telomere length and epigenomic analysis in breast cancer chemotherapy response

Size: 188 KB - Last synced at: 24 days ago - Pushed at: almost 10 years ago - Stars: 1 - Forks: 1

mdozmorov/Talk_JSM2019

Slides for JSM2019, "SpectralTAD: Defining Hierarchy of Topologically Associated Domains Using Graph Theoretical Clustering"

Size: 14.6 MB - Last synced at: 5 months ago - Pushed at: about 6 years ago - Stars: 2 - Forks: 1

mdozmorov/R.genomerunner

Scripts and examples of visualization and analysis of the enrichment and epigenomic similarity results

Language: HTML - Size: 33.4 MB - Last synced at: 5 months ago - Pushed at: almost 6 years ago - Stars: 3 - Forks: 1

mdozmorov/gwas2bed

Extracting disease-specific genomic coordinates from GWAS catalog

Language: HTML - Size: 24.9 MB - Last synced at: 5 months ago - Pushed at: over 5 years ago - Stars: 19 - Forks: 4

mdozmorov/ChIP-seq

Scripts to analyze ChIP-seq data

Language: Shell - Size: 185 KB - Last synced at: 3 months ago - Pushed at: about 5 years ago - Stars: 5 - Forks: 1

mdozmorov/Talk_HiCcompare

Slides for HiCcompareWorkshop

Language: HTML - Size: 7.04 MB - Last synced at: 5 months ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 0

mdozmorov/Talk_CHRI

Slides for the "Bioinformatics approaches for cancer genomics" talk

Language: HTML - Size: 5.96 MB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

mdozmorov/genomerunner_database

Epigenomic data for potential use in GenomeRunner

Size: 330 KB - Last synced at: 5 months ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

mdozmorov/activeranges

Expanding collection of biologically active chromatin regions as GRanges.

Language: R - Size: 177 KB - Last synced at: 5 months ago - Pushed at: about 4 years ago - Stars: 3 - Forks: 0

mdozmorov/Talk_Hi-C

An overview presentation of chromatin conformation capture technologies and analysis methods.

Size: 54.1 MB - Last synced at: 5 months ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 1

mdozmorov/Talk_preciseTAD

Slides for "preciseTAD: A transfer learning framework for 3D domain boundary prediction at base-pair resolution" presentation

Language: SCSS - Size: 8.96 MB - Last synced at: about 2 months ago - Pushed at: almost 4 years ago - Stars: 3 - Forks: 0

mdozmorov/Talk_3Dgenome

Slides for "The genome in action: Detecting and interpreting changes in the 3D genome organization" talk

Language: SCSS - Size: 21.8 MB - Last synced at: 27 days ago - Pushed at: almost 4 years ago - Stars: 5 - Forks: 1

mdozmorov/conference_template

Bioconductor conference template web site

Language: CSS - Size: 2.57 MB - Last synced at: about 2 months ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

mdozmorov/2024-04-19.TCGA

The Cancer Genomics Atlas (TCGA) and other cancer genomics resources

Language: HTML - Size: 2.76 MB - Last synced at: 5 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

mdozmorov/MDmisc

MD helper functions. Previous version at https://github.com/mdozmorov/MDgenomerunner

Language: R - Size: 73.2 KB - Last synced at: 5 months ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 0

mdozmorov/MDgenomerunner

MD functions mostly for GenomeRunner project. See MDmisc R package for MD miscellaneous functions

Language: R - Size: 935 KB - Last synced at: 3 months ago - Pushed at: over 5 years ago - Stars: 5 - Forks: 0

mdozmorov/blogs

Links to data science, bioinformatics, statistics, and machine learning resources

Size: 179 KB - Last synced at: 5 months ago - Pushed at: almost 5 years ago - Stars: 18 - Forks: 8

mdozmorov/IntroR Fork of clayford/IntroR

Intro to R workshop for UVa Library StatLab

Language: R - Size: 165 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

mdozmorov/tabix Fork of samtools/tabix

Note: tabix and bgzip binaries are now part of the HTSlib project.

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mdozmorov/d3heatmap Fork of talgalili/d3heatmap

A D3.js-based heatmap htmlwidget for R

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mdozmorov/HMP2

16S rRNA sequencing data for the HMP2 project

Language: Shell - Size: 56.2 MB - Last synced at: 5 months ago - Pushed at: about 6 years ago - Stars: 3 - Forks: 1

mdozmorov/GTEx

Playground with GTEx data

Language: R - Size: 13.7 KB - Last synced at: 2 months ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 0

mdozmorov/EuroBioC2024 Fork of kevinrue/EuroBioC2024

Language: CSS - Size: 4.01 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

mdozmorov/BIOS567

Web site for "Statistical Methods for High-throughput Genomic Data I" BIOS 567 course

Size: 264 MB - Last synced at: 5 months ago - Pushed at: over 8 years ago - Stars: 1 - Forks: 0

mdozmorov/Aging

Epigenomic enrichment analysis of age-related genomic regions

Language: R - Size: 5.88 MB - Last synced at: 3 months ago - Pushed at: over 6 years ago - Stars: 16 - Forks: 4

mdozmorov/ATAC-seq Fork of reskejak/ATAC-seq

Basic workflow for ATAC-seq analysis

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mdozmorov/ASA-VA

Web page for the Virginia chapter of American Statistical Association https://asa-va.netlify.com/

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mdozmorov/enrichR Fork of compbiomed/enrichR

A hacky little interface to call the Enrichr functional enrichment tool from R.

Language: R - Size: 22.5 KB - Last synced at: almost 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 1

mdozmorov/runHiC Fork of XiaoTaoWang/runHiC

An easy-to-use Hi-C data processing software supporting distributed computation.

Language: Python - Size: 34.5 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

mdozmorov/onco_lnc Fork of OmnesRes/onco_lnc

Language: Python - Size: 9.01 MB - Last synced at: over 2 years ago - Pushed at: over 9 years ago - Stars: 0 - Forks: 0

mdozmorov/intropolis Fork of nellore/intropolis

Exon-exon splice junctions across SRA

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mdozmorov/rmarkdown-website Fork of rstudio/rmarkdown-website

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mdozmorov/BIOS668.2018

Web site for "Statistical Methods for High-throughput Genomic Data II" BIOS 668 course, Spring 2018 https://mdozmorov.github.io/BIOS668.2018

Language: SCSS - Size: 318 MB - Last synced at: 5 months ago - Pushed at: about 1 year ago - Stars: 7 - Forks: 0

mdozmorov/BIOS691_Cancer_Bioinformatics

Course material for the BIOS691 "Cancer Bioinformatics" course, January 25 - May 7, 2021

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mdozmorov/Tools4RR Fork of kbroman/Tools4RR

Materials for a one-credit course on reproducible research

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mdozmorov/dmGWAS2 Fork of aaronwolen/dmGWAS2

A fork of dmGWAS (http://bioinfo.mc.vanderbilt.edu/dmGWAS)

Language: R - Size: 238 KB - Last synced at: over 2 years ago - Pushed at: over 9 years ago - Stars: 0 - Forks: 0

mdozmorov/web-TCGA Fork of mariodeng/web-TCGA

A light weight shiny based web app to access TCGA data

Language: R - Size: 117 KB - Last synced at: over 2 years ago - Pushed at: about 10 years ago - Stars: 0 - Forks: 0

mdozmorov/RGraphics Fork of clayford/RGraphics

Getting Started with R Graphics workshop materials

Language: R - Size: 332 KB - Last synced at: over 2 years ago - Pushed at: over 10 years ago - Stars: 0 - Forks: 0

mdozmorov/annotables Fork of stephenturner/annotables

R data package for annotating/converting Gene IDs

Language: R - Size: 55.7 MB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

mdozmorov/bios524-r-2021

"Biostatistical Computing with R" course

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mdozmorov/manuscript_template 📦

Template of a manuscript in Rmd

Language: TeX - Size: 3.26 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 2

mdozmorov/xaringan_template 📦

Building blocks for Xaringan presentation

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mdozmorov/grant_template 📦

Template for organizing grant-related material in R Markdown

Language: TeX - Size: 112 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

mdozmorov/beamer_template 📦

Beamer template for RMarkdown class presentation

Size: 671 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

mdozmorov/scTyper Fork of omicsCore/scTyper

scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data

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mdozmorov/test_cats

Test, nothing to see here

Language: R - Size: 6.84 KB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

mdozmorov/RAIDS Fork of KrasnitzLab/RAIDS

Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms

Size: 1.77 MB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

mdozmorov/genomerunner_web

Web version of GenomeRunner

Language: JavaScript - Size: 1.93 MB - Last synced at: 3 months ago - Pushed at: over 8 years ago - Stars: 11 - Forks: 5

mdozmorov/The-Art-of-Linear-Algebra Fork of kenjihiranabe/The-Art-of-Linear-Algebra

Graphic notes on Gilbert Strang's "Linear Algebra for Everyone"

Language: TeX - Size: 23.2 MB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

mdozmorov/63_immune_cells

Gene expression profiles of 63 immune cell types

Language: R - Size: 13.1 MB - Last synced at: 3 months ago - Pushed at: almost 8 years ago - Stars: 2 - Forks: 6

mdozmorov/oncoEnrichR Fork of sigven/oncoEnrichR

Cancer-dedicated gene set interpretation

Language: R - Size: 1.63 GB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

mdozmorov/R.Lorin.RNA-seq

Interpretation of RNA-seq data

Language: R - Size: 15.5 MB - Last synced at: about 2 months ago - Pushed at: about 11 years ago - Stars: 2 - Forks: 1

mdozmorov/Talk_Genomics

Talk for the Science Club, Department of Pathology, VCU. May 15, 2019.

Size: 17.8 MB - Last synced at: 5 months ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 0

mdozmorov/Talk_ISMB2020

TADcompare abstract for the virtual ISMB 2020 conference

Size: 1.28 MB - Last synced at: 5 months ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

mdozmorov/ATACseqQCWorkshop Fork of haibol2016/ATACseqQCWorkshop

ATACseqQC tutorials for BioC 2019 workshop

Language: HTML - Size: 72.9 MB - Last synced at: over 2 years ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

mdozmorov/CreateAPackage Fork of Kayla-Morrell/CreateAPackage

Size: 51.8 KB - Last synced at: over 2 years ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

mdozmorov/PCAworkshop Fork of aedin/PCAworkshop

A introduction to PCA in R

Language: Dockerfile - Size: 32.2 KB - Last synced at: over 2 years ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

mdozmorov/ci-workshop Fork of gilesc/ci-workshop

R/Bioconductor cancer informatics workshop at Rajiv Gandhi Centre in January 2013

Language: R - Size: 52 MB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 2

mdozmorov/Talk_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.

Language: JavaScript - Size: 14.3 MB - Last synced at: about 2 months ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 1

mdozmorov/liftOver_test

liftOver example

Size: 348 KB - Last synced at: 5 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

mdozmorov/presentations

Talks and related material

Language: CSS - Size: 140 MB - Last synced at: 3 months ago - Pushed at: over 7 years ago - Stars: 6 - Forks: 2