Discover mdozmorov/Grants_notes Open Source project

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Created almost 6 years ago
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Notes on potential funding opportunities

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

MDnotes

Links to all data science, genomics, and other notes

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

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/Grants_notes

mdozmorov

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