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BgeeDB /bgee_pipeline

Source code of the Bgee pipeline used to build the Bgee database

python java gene rna-seq pipeline makefile biology perl gene-expression expression transcriptomics est affymetrix in-situ-hybridization

UpdatedMar 17, 2025
Perl

HenrikBengtsson /aroma.affymetrix

🔬 R package: Analysis of Large Affymetrix Microarray Data Sets

package r analysis hpc notebook dna expression microarray rna reproducibility large-scale affymetrix copy-number

UpdatedMar 15, 2025
R

hernanmd /BioScripts

A collection of miscellaneous bioinformatics scripts

bash bioinformatics illumina cnv affymetrix shapeit2

UpdatedFeb 28, 2020
Smalltalk

SiYangming /simpleaffy

backup forhttps://www.bioconductor.org/packages/3.12/bioc/html/simpleaffy.html

bioinformatics r affymetrix affy

UpdatedJun 13, 2022
R

gustaveroussy /apt.oncoscan.2.4.0

Affymetrix OncoScan / OncoScan_CNV processing using apt-copynumber-onco-ssa (2.4.0)

r microarray normalization affymetrix

UpdatedDec 6, 2018
R

CNuge /miscellaneous_scripts

Various python programs I use for the manipulation of SNP genotype datasets and other bioinformatics tasks. This repository features miscellaneous scripts to help work efficiently in common bioinformatics tasks I encounter. Use at own risk

microarray-data miscellaneous-scripts affymetrix snp-file snp-data snp-genotype-datasets bioinformatics-tasks microarray-design

UpdatedApr 6, 2018
Python

cemordaunt /AutismCordBloodExpression

Analysis of gene expression in umbilical cord blood from ASD, Non-TD, and TD subjects in the MARBLES and EARLI studies

gene-expression microarray autism meta-analysis affymetrix

UpdatedJan 12, 2022
R

uribalb /genex

Gene expression experiments using Python and R

python data-science r deep-learning jupyter genomics tensorflow pipelines gene-expression pandas dask affymetrix

UpdatedApr 13, 2018
HTML

HenrikBengtsson /Affx-Fusion-SDK

🔬 Affymetrix Fusion Software Developers Kit (SDK)

UpdatedNov 30, 2014
C++

roman-tremmel /Affymetrix-HTA2.0-Transcript-cluster-annotation

App to illustrate the history of transcript cluster annotations of the Affy array HTA2.0

app annotation shiny id probe transcript affymetrix hta2

UpdatedMay 28, 2020
R

gustaveroussy /apt.cytoscan.2.4.0

Affymetrix CytoScan (750k / HD) processing using apt-copynumber-cyto-ssa (2.4.0)

r microarray normalization affymetrix

UpdatedJul 8, 2024
R

tpoorten /leaf_print

R scripts & functions for SNP data analysis of genotyping data from Affymetrix Axiom arrays

r snps affymetrix

UpdatedJun 1, 2018
R

cnr-ibba /SMARTER-database

Smarter database repository

database efficiency plink breeding genotype smarter resilience affymetrix ruminant

UpdatedOct 16, 2024
Jupyter Notebook

paulstothard /genotype_conversion_file_builder

A pipeline for determining the genomic location and transformation rules for the variants described in Illumina or Affymetrix genotype panel manifest files.

bioinformatics nextflow illumina affymetrix genotypes genotype-conversion

UpdatedJul 11, 2024
Perl

fboulnois /made

Microarray Analysis of Differential Expression

r genome microarray illumina differential-expression affymetrix

UpdatedApr 7, 2016
R

hernanmd /SSNPs_WCF2018

Find shared SNPs between different microarray chips

bash bioinformatics snps illumina affymetrix microarrays

UpdatedMar 27, 2018
Shell

xindong95 /DEAP

Differential Expression Analysis Pipeline

snakemake pipeline biology rnaseq microarray illumina affymetrix

UpdatedAug 22, 2024
Python

genepattern /AffySTExpressionFileCreator

Creates a GCT file from a set of CEL files from Affymetrix ST arrays.

utility preprocess affymetrix genepattern-module

UpdatedJul 26, 2021
R

gustaveroussy /apt.snp6.1.20.0

Affymetrix GenomeWideSNP_6 processing using apt-copynumber-workflow (1.20.0)

r microarray normalization affymetrix

UpdatedDec 6, 2018
R

zqzneptune /affyio

Updated version to handle CEL files

microarray affymetrix

UpdatedJun 10, 2023
C

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