microarray

There are 3 repositories under microarray topic.

mikelove / bioc-refcard
Bioconductor cheat sheet
bioconductor bioinformatics r rnaseq compbio guide howto cheatsheet microarray
Language:HTML 191
guma44 / GEOparse
Python library to access Gene Expression Omnibus Database (GEO)
geo-database high-throughput-sequencing htseq microarray bioinformatics rna-sequencing rna-seq
Language:Jupyter Notebook 155
nf-core / differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
nextflow nf-core pipeline workflow atac-seq chip-seq deseq2 differential-abundance differential-expression gsea limma microarray rna-seq shiny
Language:Nextflow 84
zwdzwd / sesame
🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips
dna-methylation bioinformatics microarray
Language:R 79
greenelab / TDM
R package for normalizing RNA-seq data to make them comparable to microarray data.
r package rna-seq microarray data-processing
Language:R 40
greenelab / RNAseq_titration_results
Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
bioinformatics rnaseq microarray normalization machine-learning cancer supplement analysis gene-expression
Language:HTML 37
gustaveroussy / EaCoN
Easy Copy Number !
r copy-number microarray exome-sequencing segmentation
Language:R 21
allielarocco / Microarray-Analysis
Microarray Analysis Pipeline in Python
microarray microarray-studies microarray-experiments pipeline enrichment-analysis differential-expression differentially-expressed-genes ncbi-geo ncbi-database ncbi-submission
Language:Jupyter Notebook 19
Bohdan-Khomtchouk / HeatmapGenerator
Cross-platform GUI desktop application for making biological heatmaps
heatmap rna-seq microarray gui-application computational-biology opengl lightweight c-plus-plus r-programming
Language:C 19
HenrikBengtsson / aroma.affymetrix
🔬 R package: Analysis of Large Affymetrix Microarray Data Sets
r package affymetrix copy-number expression dna rna analysis microarray large-scale reproducibility hpc notebook
Language:R 12
dlaperriere / GEO_microarrays
analyze_geo_microarrays.py : Differential expression analysis of published microarrays datasets from the NCBI Gene Expression Omnibus (GEO)
microarray limma bioinformatics ncbi-geo
Language:Python 11
Pytorch-UNet-2
upashu1 / Pytorch-UNet-2
UNet 2.0 - Pytorch implementation of the U-Net 2.0 for image semantic segmentation, with processing blocks for noisy images
unet-image-segmentation unet-pytorch unet unet-model unet2 microarray image-segmentation microarray-image-segmentation-cnn microarray-deep-learning pytorch image-segmenation-unet cnn
Language:Python 9
ahmedmoustafa / gene-expression-datasets
Collection of gene expression datasets
microarray-data microarray microarray-data-analysis gene-expression transciptomics rna-seq rna-seq-datasets datasets
8
tarlaun / BioInf_Project
Bioinformatics course project - Fall 2020, analysis of genetic expression omnibus (GEO) data series of Acute Myeloid Leukemia
aml geoparse genetic-expression-omnibus bioinformatics acute-myeloid-leukemia microarray-data microarray-data-analysis microarray
Language:Python 8
DoubleHelixApp / DoubleHelix
Genomic data manipulation tool
bioinformatics genome genome-analysis genomics microarray wgs bam-files cram-files genetics sam-files whole-genome-sequencing
Language:Python 6
shyammarjit / SAGA
SAGA: Simulated annealing aided genetic algorithm for gene selection from microarray data
feature-selection gene genetic-algorithm microarray omics simulated-annealing
Language:Jupyter Notebook 5
viktormiok / PhD-thesis
Latex scripts to compile my PhD thesis
multivariate-timeseries splines ridge-regression rna-seq microarray cervical-cancer gene-regulatory-network-inference
Language:TeX 5
CNAG-Biomedical-Informatics / beacon2-cbi-tools
Beacon v2 - CNAG Biomedical Informatics - Tools (Data ingestion tools)
beacon beacon-friendly-format beacon-v2 bff json mongodb phenopackets-v2 pxf vcf beacon2-ri-tools beacon2-reference-implementation beacon2-ri cnag data-exchange browser bff-portal 23andme microarray snp
Language:Perl 3
Honchkrow / Deconer
Deconer: A Comprehensive and Systematic Cell Type Deconvolution Evaluator
deconvolution gene-expression microarray rna-seq scrna-seq single-cell cell-type-deconvolution
Language:R 3
idssplab / overall_survival_nsclc
bimodal DNN for NSCLC patient overall survival prediction
deep-learning deep-neural-networks bioinformatics bimodal-multicast biomarkers non-small-cell-lung-cancer microarray clinical-data prognostic-biomarkers overall-survival-prediction
3
TCP-Lab / bioTEA
bioTEA - A user friendly tool to perform transcript expression analysis
bioinformatics-tool command-line-tool differential-gene-expression docker linux microarray python transcriptomics
Language:Python 3
viktormiok / BioFig
R package for visualization of omics data
rna-seq microarray proteomics quality-control
Language:R 3
viktormiok / tigaR
Temporal Integrative Genomics Analysis in R
differential-gene-expression inla empirical-bayes microarray rna-seq
Language:R 3
viktormiok / tigaRcycle
An R package for utilities to guide in-depth detection of circadian signals from omics time series data
r circadian-rhythmicity cycling omics-data microarray rna-seq
Language:Jupyter Notebook 3
XPRESSyourself / XPRESSplot
A toolkit for navigating and analyzing gene expression datasets
rna-seq microarray rnaseq plotting analysis visualization genomics
Language:Python 3
adimascf / idat2plink
A simple program to generate .vcf and plink format files from .idat files
bioinformatics command-line-tool microarray illumina
Language:Shell 2
alexvpickering / revigoR
scrape REVIGO Gene Ontology web app and plot results
gene-ontology rna-seq microarray
Language:R 2
draeger-lab / InCroMAP
Integrated analysis of Cross-platform MicroArray and Pathway data
microarray pathway-analysis visualization data-integration
Language:Java 2
GrosseLab / BGSC
Bayesian Gene Selection Criterion (BGSC) approach
microarray differential-gene-expression reproducible-research r statistical-models
Language:R 2
michaeltneylon / spark_rma
SparkRMA: Robust Multi-array Average (RMA) In Apache Spark
microarray rma spark preprocessing scalable
Language:Python 2
qPCR4vir / VisualOliDeg
design of primers and probes for PCR/microarray by visual selection from aligned DNA sequences
pcr microarray primer excel workbook bioinformatics science aligned-dna-sequences
Language:Visual Basic 2
viktormiok / PhD-thesisSM
PhD thesis supplementary materials
multivariate-timeseries splines ridge-regression rna-seq microarray cervical-cancer
Language:TeX 2
lnv-louis / AML-Subtypes-Classification-ML
R scripts for RF and RBF-SVM for Acute Myeloid Leukemia subtypes multiclass classification using gene expression profiles. LASSO feature selection, SMOTE sampling, 10-fold cross-validation, variable importance plot, PCA plot, normalized Confusion Matrix, GSE13159.
bioinformatics biomarkers classification data-mining gene-expression machine-learning microarray random-forest supervised-learning aml-subtypes confusion-matrix-heatmap pca-analysis rbf-kernel support-vector-machines variable-importance-plots
Language:R 1
RGLab / HIPCMatrix
Utilities for processing and analyzing HIPC gene expression data in ImmuneSpace
immunespace immport hipc microarray rna-seq
Language:R 1
SamThilmany / microarray-analysis_treatment-kinetics
This R script is used to analyze microarray data acquired by an Agilent SureScan Microarray Scanner.
limma microarray microarray-data microarray-data-analysis r
Language:R 1
tiagochavo87 / LCSH_analysis
Analysis of long continuous stretches of homozygosity of the human genome.
bioinformatics bioinformatics-analysis cromosome genome-analysis homozygosity lcsh microarray microarray-data-analysis python
Language:Jupyter Notebook 1

microarray

mikelove / bioc-refcard

guma44 / GEOparse

nf-core / differentialabundance

zwdzwd / sesame

greenelab / TDM

greenelab / RNAseq_titration_results

gustaveroussy / EaCoN

allielarocco / Microarray-Analysis

Bohdan-Khomtchouk / HeatmapGenerator

HenrikBengtsson / aroma.affymetrix

dlaperriere / GEO_microarrays

upashu1 / Pytorch-UNet-2

ahmedmoustafa / gene-expression-datasets

tarlaun / BioInf_Project

DoubleHelixApp / DoubleHelix

shyammarjit / SAGA

viktormiok / PhD-thesis

CNAG-Biomedical-Informatics / beacon2-cbi-tools

Honchkrow / Deconer

idssplab / overall_survival_nsclc

TCP-Lab / bioTEA

viktormiok / BioFig

viktormiok / tigaR

viktormiok / tigaRcycle

XPRESSyourself / XPRESSplot

adimascf / idat2plink

alexvpickering / revigoR

draeger-lab / InCroMAP

GrosseLab / BGSC

michaeltneylon / spark_rma

qPCR4vir / VisualOliDeg

viktormiok / PhD-thesisSM

lnv-louis / AML-Subtypes-Classification-ML

RGLab / HIPCMatrix

SamThilmany / microarray-analysis_treatment-kinetics

tiagochavo87 / LCSH_analysis