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1
Moderated estimation of fold change and dispersion for RNA-seq ...
https://pubmed.ncbi.nlm.nih.gov/25516281/
2
Moderated estimation of fold change and dispersion for RNA-seq ...
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8
3
Three Differential Expression Analysis Methods for RNA Sequencing
https://pubmed.ncbi.nlm.nih.gov/34605806/
4
Analyzing RNA-seq data with DESeq2 - Bioconductor
https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
5
An evaluation of RNA-seq differential analysis methods - PMC
https://pmc.ncbi.nlm.nih.gov/articles/PMC9480998/
6
PyDESeq2: a python package for bulk RNA-seq differential ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC10502239/
7
SARTools: A DESeq2- and EdgeR-Based R Pipeline for ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC4900645/
11
DESeq2 Returning Nucleotides As Gene ID - Galaxy Help
https://help.galaxyproject.org/t/deseq2-returning-nucleotides-as-gene-id/8902
12
mirrorCheck: an R package facilitating informed use of DESeq2's ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC12089695/
13
Best way to export transcriptomic data from NCBI GEO for analysis ...
https://www.researchgate.net/post/Best_way_to_export_transcriptomic_data_from_NCBI_GEO_for_analysis_with_DESeq2_in_R
14
How to input data and metadata from NCBI for RNA-Seq analysis in R
https://bioinformatics.stackexchange.com/questions/18370/how-to-input-data-and-metadata-from-ncbi-for-rna-seq-analysis-in-r
15
RNA-Seq differential expression analysis: An extended review and a ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC5739479/
16
RNA sequencing data analysis - Counting, normalization ... - STHDA
https://www.sthda.com/english/wiki/wiki.php?id_contents=7289
17
7 201: RNA-seq data analysis with DESeq2 - GitHub Pages
https://bioconductor.github.io/BiocWorkshops/rna-seq-data-analysis-with-deseq2.html
18
DESeq2 Black Box : r/bioinformatics - Reddit
https://www.reddit.com/r/bioinformatics/comments/tf59r1/deseq2_black_box/
19
cwl-ngs-workflows-cbb/tools/R/deseq2-2conditions.cwl at master
https://github.com/ncbi/cwl-ngs-workflows-cbb/blob/master/tools/R/deseq2-2conditions.cwl
21
Gene-level differential expression analysis with DESeq2
https://hbctraining.github.io/DGE_workshop/lessons/04_DGE_DESeq2_analysis.html
22
Differential expression analysis for sequence count data
https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-10-r106
24
Differential gene expression analysis pipelines and bioinformatic ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC10951429/
25
Google Scholar
https://scholar.google.com/scholar_lookup?title=Moderated%2Bestimation%2Bof%2Bfold%2Bchange%2Band%2Bdispersion%2Bfor%2BRNA-seq%2Bdata%2Bwith%2BDESeq2&author=Love,%2BM.I.&author=Huber,%2BW.&author=Anders,%2BS.&publication_year=2014&journal=Genome%2BBiol.&volume=15&pages=550&doi=10.1186/s13059-014-0550-8
26
DESeq2: An Overview of a Popular RNA-Seq Analy... | Pluto Bio
https://pluto.bio/resources/Learning%20Series/deseq2-an-overview-of-popular-rna-seq-analysis-package
27
Moderated estimation of fold change and dispersion for RNA-seq ...
https://www.bibsonomy.org/bibtex/20499d28f9c10ed63559a923531f4b1bb/marcsaric
28
DESeq2 and Geo2R workflow tutorial | Differential Gene Expression ...
https://www.youtube.com/watch?v=ae1kuulISHQ
29
RNA-Seq differential expression work flow using DESeq2 - STHDA
https://www.sthda.com/english/wiki/rna-seq-differential-expression-work-flow-using-deseq2
30
stat.DESeq function - RDocumentation
https://www.rdocumentation.org/packages/caRpools/versions/0.83/topics/stat.DESeq
31
RNA-seq Analysis in R
https://sbc.shef.ac.uk/prostate-bioinformatics/rna-seq-annotation-visualisation.nb.html
32
IBE DESEQ2 RNAseq tutorial NCBI GEO2R | Kaggle
https://www.kaggle.com/code/babumiaphd/ibe-deseq2-rnaseq-tutorial-ncbi-geo2r
33
Differential Gene Expression Analysis with Kallisto & DESeq2 - AWS
https://rstudio-pubs-static.s3.amazonaws.com/1041443_0d95b5f9d0de43f8bbc1aaed6b4ed8d2.html
34
SARTools: A DESeq2- and EdgeR-Based R Pipeline for ... - PubMed
https://pubmed.ncbi.nlm.nih.gov/27280887/
35
How to download RNA-Seq data from NCBI GEO - YouTube
https://www.youtube.com/watch?v=2RFYKTvCXHs&pp=ygUGI3NjZGVn
36
thelovelab/DESeq2: Differential expression of RNA-seq ... - GitHub
https://github.com/thelovelab/DESeq2
38
DESeq2 - Illumina Support Center
https://support.illumina.com/help/BS_App_RNASeq_DE_OLH_1000000071939/Content/Source/Informatics/DESeq2.htm
39
Analyzing RNA-Seq Data from Chlamydia with Super Broad ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC11142123/
40
DESeq2 workflow tutorial | Differential Gene Expression Analysis
https://www.youtube.com/watch?v=KJDnk6Glbgg
42
Polyethylene terephthalate (PET) primary degradation products ...
https://journals.asm.org/doi/abs/10.1128/spectrum.00181-25?af=R
43
Assessment of plasma derived microbiome profiles in lung cancer ...
https://www.nature.com/articles/s41540-025-00536-8
44
Dual roles of Anisakis pegreffii proteins in macrophage immune ...
https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2025.1595093/full
45
Dissolved organic matter and sulfide enhance the CH4 consumption ...
https://journals.asm.org/doi/abs/10.1128/spectrum.03133-24?af=R
47
Taurine from tumour niche drives glycolysis to promote ... - Nature
https://www.nature.com/articles/s41586-025-09018-7
48
Sesquiterpenoid Hormones Farnesoic Acid and Methyl ... - MDPI
https://www.mdpi.com/2218-273X/15/6/815
50
Loss of Myostatin Alters Gut Microbiota and Carbohydrate ... - MDPI
https://www.mdpi.com/2306-7381/12/6/560
51
In Papyro Comparison of TMM (edgeR), RLE (DESeq2), and MRN ...
https://pubmed.ncbi.nlm.nih.gov/27695478/
53
Error estimates for the analysis of differential expression from RNA ...
https://pubmed.ncbi.nlm.nih.gov/25337456/
59
A transcriptome software comparison for the analyses of treatments ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC9208185/
60
An evaluation of RNA-seq differential analysis methods - PubMed
https://pubmed.ncbi.nlm.nih.gov/36112652/
61
Identification of key differentially expressed genes in SARS-CoV-2 ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC10036311/
62
Differential expression analysis for sequence count data - PubMed
https://pubmed.ncbi.nlm.nih.gov/20979621/
64
Computational identification of differentially-expressed genes as ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC10259169/
65
RNA-Seq workflow: gene-level exploratory analysis and differential ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC4670015/
66
Optimization of an RNA-Seq Differential Gene Expression Analysis ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC5817962/
67
Comparative analysis of differential gene expression analysis tools ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC6339299/
69
Differentially expressed genes of RNA-seq data are suggested on ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC10776424/
70
Differential Expression Analysis for RNA-Seq: An Overview of ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC4678998/
71
How well do RNA-Seq differential gene expression tools perform in ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC6748783/
73
Interpretation of differential gene expression results of RNA-seq data
https://pmc.ncbi.nlm.nih.gov/articles/PMC6954399/
74
Comparison of software packages for detecting differential ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC4293378/
75
Benchmarking differential expression analysis tools for RNA-Seq
https://pmc.ncbi.nlm.nih.gov/articles/PMC6052553/
76
Robustly detecting differential expression in RNA sequencing data ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC4066750/
77
Choice of library size normalization and statistical methods for ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC6986029/
78
DEclust: A statistical approach for obtaining differential expression ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC5697878/
79
Winsorization greatly reduces false positives by popular differential ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC11523781/
81
NCBI-generated RNA-seq count dataBETA - GEO
https://www.ncbi.nlm.nih.gov/geo/info/rnaseqcounts.html
82
Bacterial Differential Expression Analysis Methods - PubMed
https://pubmed.ncbi.nlm.nih.gov/32720149/
83
Brief guide to RNA sequencing analysis for nonexperts in ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC11091515/
84
edgeRun: an R package for sensitive, functionally relevant ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC4514933/
85
Power analysis and sample size estimation for RNA-Seq differential ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC4201821/
86
a python package for bulk RNA-seq differential expression analysis
https://pubmed.ncbi.nlm.nih.gov/37669147/
87
An evaluation of statistical differential analysis methods in single-cell ...
https://pubmed.ncbi.nlm.nih.gov/36993457/
88
Gene Expression Counts on NCBI RefSeq Eukaryotic Genomes
https://ncbiinsights.ncbi.nlm.nih.gov/2023/11/20/gene-expression-counts-refseq-eukaryotic-genomes/
89
dearseq: a variance component score test for RNA-seq differential ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC7676475/
90
Error estimates for the analysis of differential expression from RNA ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC4179614/
91
How many biological replicates are needed in an RNA-seq ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC4878611/
92
A Comparative Study of Techniques for Differential Expression ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC4132098/
94
A comprehensive workflow for optimizing RNA-seq data analysis
https://pmc.ncbi.nlm.nih.gov/articles/PMC11197194/
96
Comparison of RNA Sequencing Data Alignment and Gene ...
https://pmc.ncbi.nlm.nih.gov/articles/PMC6617288/
98
Integrated COVID-19 Predictor: Differential expression analysis to ...
https://pubmed.ncbi.nlm.nih.gov/35687925/