limma
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Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
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Nov 4, 2024 - Nextflow
DEqMS is a tool for quantitative proteomic analysis
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Jun 1, 2020 - R
Tools for normalization, evaluation of outliers, technical biases and batch effects and differential expression analysis.
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Oct 17, 2024 - R
A Snakemake workflow for performing and visualizing differential expression analyses (DEA) on NGS data powered by the R package limma.
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Oct 18, 2024 - R
A quick recap of widely used differential analyses methods in R for RNA-seq experiments
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Mar 12, 2020
Differential expression analysis: DESeq2, edgeR, limma. Realized in python based on rpy2
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May 7, 2021 - Jupyter Notebook
analyze_geo_microarrays.py : Differential expression analysis of published microarrays datasets from the NCBI Gene Expression Omnibus (GEO)
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Aug 1, 2021 - Python
Simple workflows for the isobaric-labeling proteomic data from Proteome Discoverer with ANOVA, t-testing, DEqMS/limma and annotation via fgsea
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May 19, 2022 - R
EuroBioc2020 SPEAQeasy workshop https://eurobioc2020.bioconductor.org by Nick Eagles and Josh Stolz. For more information about SPEAQeasy check http://research.libd.org/SPEAQeasy/. For an example on how to use this RNA-seq processing pipeline and analyze the output files check http://research.libd.org/SPEAQeasy-example/.
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Dec 16, 2020 - R
A selection of analytical approaches, tools, and utilities for the processing of microbiome data derived from either 16S rRNA amplicon sequencing or shotgun metagenomics.
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Feb 8, 2024 - R
Bioinformatic analysis of gene expression microarray profiles and DGEs on R and R studio
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Jul 17, 2024 - Jupyter Notebook
GSE147507 SARS-Cov-2 Dataset from Mt. Sinai
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Apr 4, 2020
This R script is used to analyze microarray data acquired by an Agilent SureScan Microarray Scanner.
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Jan 13, 2023 - R
Timeseries analysis of -omics data can be carried out by fitting spline curves to the data and using limma for hypothesis testing. For this, the right spline freedom and further hyperparameters must be identified, and the obtained hits clustered based on the spline shape.The R package SplineOmics streamlines this whole process and generates reports
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Oct 29, 2024 - R
Provides easy to use, objective oriented functions for preprocessing methylation data produced by an Illumina Infinium BeadChip and detecting differentially methylated positions and regions within the DNA.
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Apr 17, 2023 - R
This scripts involves five major steps including GEO dataset download, data normalization, data manipulation, fetching phenodata and feature data and differentially expressed genes (DEGs) analysis using R and bioconductor packages.
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Feb 27, 2023 - R
Tuberculosis@LOG and NPR, Macrophage gene expression time series.
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Oct 25, 2017 - Python
Differential Gene Expression (DGE) Analysis in Curated Microarray Data of Breast Cancer Subtypes
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Oct 30, 2023 - R
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