• Stars
    star
    1
  • Language
  • License
    MIT License
  • Created over 5 years ago
  • Updated over 2 years ago

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

Lists of publicly available datasets for machine learning

More Repositories

1

scRNA-seq_notes

A list of scRNA-seq analysis tools
R
510
star
2

HiC_tools

A collection of tools for Hi-C data analysis
482
star
3

MachineLearning_notes

Machine learning and deep learning resources
401
star
4

HiC_data

A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
166
star
5

TCGAsurvival

Scripts to analyze TCGA data
R
113
star
6

Cancer_notes

A continually expanding collection of cancer genomics notes and data
92
star
7

Statistics_notes

Statistics, data analysis tutorials and learning resources
72
star
8

scATAC-seq_notes

scATAC-seq data analysis tools and papers
67
star
9

Immuno_notes

Immunology-related bioinformatics data and tools
61
star
10

scHiC_notes

Notes on single-cell Hi-C technologies, tools, and data
54
star
11

MDnotes

Links to all data science, genomics, and other notes
37
star
12

RNA-seq_notes

A continually expanding collection of RNA-seq tools
33
star
13

Brain_genomic_data

Brain-related -omics data
22
star
14

SNP_notes

Notes on SNP-related tools and genome variation analysis
20
star
15

gwas2bed

Extracting disease-specific genomic coordinates from GWAS catalog
HTML
18
star
16

ChIP-seq_notes

Notes on ChIP-seq and other-seq-related tools
17
star
17

blogs

Links to data science, bioinformatics, statistics, and machine learning resources
16
star
18

Aging

Epigenomic enrichment analysis of age-related genomic regions
R
15
star
19

Microbiome_notes

A continually expanding collection of microbiome analysis tools
14
star
20

RNA-seq

RNA-seq analysis scripts
R
14
star
21

Aging_clock

Data and papers related to epigenetic clocks predicting age
R
12
star
22

HiCcompareWorkshop

Differential Hi-C Data Analysis Workshop https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.76
Dockerfile
12
star
23

genomerunner_web

Web version of GenomeRunner
JavaScript
11
star
24

R_notes

Data science in R notes
9
star
25

Programming_notes

Programming-related notes
8
star
26

Methylation_notes

Notes on DNA methylation analysis
8
star
27

bioinformatics-impact

GitHub statistics as a measure of the impact of open-source bioinformatics software
TeX
7
star
28

E-MTAB-3610

Processed E-MTAB-3610 dataset - Transcriptional Profiling of 1,000 human cancer cell lines
R
7
star
29

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
7
star
30

presentations

Talks and related material
CSS
6
star
31

Python_notes

Data science in Python notes
5
star
32

manuscript_template

Template of a manuscript in Rmd
TeX
5
star
33

Jobs_notes

Notes for job seekers
5
star
34

promoter_extract

Extract genomic coordinates of the promoters from a list of genes.
Python
4
star
35

ChIP-seq

Scripts to analyze ChIP-seq data
Shell
4
star
36

BIOS691_Cancer_Bioinformatics

Course material for the BIOS691 "Cancer Bioinformatics" course, January 25 - May 7, 2021
HTML
4
star
37

Talk_3Dgenome

Slides for "The genome in action: Detecting and interpreting changes in the 3D genome organization" talk
SCSS
4
star
38

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.
R
4
star
39

MDgenomerunner

MD functions mostly for GenomeRunner project. See MDmisc R package for MD miscellaneous functions
R
4
star
40

bios524-r-2021

"Biostatistical Computing with R" course
HTML
3
star
41

BIOS691_deep_learning_R

"Deep Learning with R" course material
HTML
3
star
42

HMP2

16S rRNA sequencing data for the HMP2 project
Shell
3
star
43

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
3
star
44

MDmisc

MD helper functions. Previous version at https://github.com/mdozmorov/MDgenomerunner
R
2
star
45

R.genomerunner

Scripts and examples of visualization and analysis of the enrichment and epigenomic similarity results
HTML
2
star
46

dcaf

Misc. scripts and examples
Shell
2
star
47

Grants_notes

Notes on potential funding opportunities
2
star
48

activeranges

Expanding collection of biologically active chromatin regions as GRanges.
R
2
star
49

GTEx

Playground with GTEx data
R
2
star
50

63_immune_cells

Gene expression profiles of 63 immune cell types
R
2
star
51

R.Lorin.RNA-seq

Interpretation of RNA-seq data
R
2
star
52

Talk_preciseTAD

Slides for "preciseTAD: A transfer learning framework for 3D domain boundary prediction at base-pair resolution" presentation
SCSS
2
star
53

GenomeRunner

Automating genome exploration
Visual Basic
1
star
54

Talk_Genomics

Talk for the Science Club, Department of Pathology, VCU. May 15, 2019.
1
star
55

PCAworkshop

A introduction to PCA in R
Dockerfile
1
star
56

deconvolution

Cell type-specific deconvolution of 'omics' data
R
1
star
57

Talk_JSM2019

Slides for JSM2019, "SpectralTAD: Defining Hierarchy of Topologically Associated Domains Using Graph Theoretical Clustering"
1
star
58

Methylation850K

Methylation analysis of Illumina 850K arrays
R
1
star
59

beamer_template

Beamer template for RMarkdown class presentation
1
star
60

Talk_ISMB2020

TADcompare abstract for the virtual ISMB 2020 conference
1
star
61

grdocs

GenomeRunner documentation
TeX
1
star
62

R.-ChIP-seq.histone

Analysis of histone marks, and their differential presence in the genome
R
1
star
63

Talk_HiCcompare

Slides for HiCcompareWorkshop
HTML
1
star
64

R.Sjogren

Sjogren syndrome microarray data analysis
HTML
1
star
65

lecture1

Test repo
1
star
66

BIOS567

Web site for "Statistical Methods for High-throughput Genomic Data I" BIOS 567 course
1
star
67

PathwayRunner

PathwayRunner computed enrichment of gene set(s) in all pathways using hypergeometric test
R
1
star
68

GDS-processor

Process GDS files from Gene Expression Omnibus (GEO)
Visual Basic
1
star
69

Talk_Hi-C

An overview presentation of chromatin conformation capture technologies and analysis methods.
1
star
70

Quantile-normalization

Quantile normalization of gene expression matrix with missing values
Visual Basic
1
star
71

RepeatSoaker

a simple method to eliminate low-complexity short reads
Makefile
1
star
72

BIOS567.2017

Web site for "Statistical Methods for High-throughput Genomic Data I" BIOS 567 course, Fall 2017
SCSS
1
star