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Links to all data science, genomics, and other notes

scRNA-seq_notes

A list of scRNA-seq analysis tools

510

HiC_tools

A collection of tools for Hi-C data analysis

482

MachineLearning_notes

Machine learning and deep learning resources

401

HiC_data

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

166

TCGAsurvival

Scripts to analyze TCGA data

113

Cancer_notes

A continually expanding collection of cancer genomics notes and data

Statistics_notes

Statistics, data analysis tutorials and learning resources

scATAC-seq_notes

scATAC-seq data analysis tools and papers

Immuno_notes

scHiC_notes

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

RNA-seq_notes

A continually expanding collection of RNA-seq tools

Brain_genomic_data

Brain-related -omics data

SNP_notes

gwas2bed

Extracting disease-specific genomic coordinates from GWAS catalog

HTML

ChIP-seq_notes

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

blogs

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

Aging

Epigenomic enrichment analysis of age-related genomic regions

Microbiome_notes

A continually expanding collection of microbiome analysis tools

RNA-seq

RNA-seq analysis scripts

Aging_clock

Data and papers related to epigenetic clocks predicting age

HiCcompareWorkshop

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

Dockerfile

genomerunner_web

Web version of GenomeRunner

JavaScript

R_notes

Data science in R notes

Programming_notes

Programming-related notes

Methylation_notes

Notes on DNA methylation analysis

bioinformatics-impact

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

TeX

E-MTAB-3610

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

BIOS668.2018

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

SCSS

presentations

Talks and related material

CSS

Python_notes

Data science in Python notes

manuscript_template

Template of a manuscript in Rmd

TeX

Jobs_notes

Notes for job seekers

promoter_extract

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

Python

ChIP-seq

Scripts to analyze ChIP-seq data

Shell

BIOS691_Cancer_Bioinformatics

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

HTML

Talk_3Dgenome

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

SCSS

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.

MDgenomerunner

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

bios524-r-2021

"Biostatistical Computing with R" course

HTML

BIOS691_deep_learning_R

"Deep Learning with R" course material

HTML

HMP2

16S rRNA sequencing data for the HMP2 project

Shell

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.

JavaScript

MDmisc

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

R.genomerunner

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

HTML

dcaf

Misc. scripts and examples

Shell

Grants_notes

Notes on potential funding opportunities

activeranges

Expanding collection of biologically active chromatin regions as GRanges.

GTEx

Playground with GTEx data

63_immune_cells

Gene expression profiles of 63 immune cell types

R.Lorin.RNA-seq

Interpretation of RNA-seq data

Talk_preciseTAD

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

SCSS

GenomeRunner

Automating genome exploration

Visual Basic

Talk_Genomics

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

deconvolution

Cell type-specific deconvolution of 'omics' data

Talk_JSM2019

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

Methylation850K

Methylation analysis of Illumina 850K arrays

beamer_template

Beamer template for RMarkdown class presentation

Talk_ISMB2020

TADcompare abstract for the virtual ISMB 2020 conference

grdocs

GenomeRunner documentation

TeX

R.-ChIP-seq.histone

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

Talk_HiCcompare

Slides for HiCcompareWorkshop

HTML

R.Sjogren

Sjogren syndrome microarray data analysis

HTML

lecture1

Test repo

BIOS567

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

Data_notes

Lists of publicly available datasets for machine learning

PathwayRunner

PathwayRunner computed enrichment of gene set(s) in all pathways using hypergeometric test

GDS-processor

Process GDS files from Gene Expression Omnibus (GEO)

Visual Basic

Talk_Hi-C

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

Quantile-normalization

Quantile normalization of gene expression matrix with missing values

Visual Basic

RepeatSoaker

a simple method to eliminate low-complexity short reads

Makefile

BIOS567.2017

Web site for "Statistical Methods for High-throughput Genomic Data I" BIOS 567 course, Fall 2017

SCSS

mdozmorov/MDnotes

mdozmorov

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