Overview on used software and Databases
Softwares and algorithms	Ref.	Source Identifier
conda 24.3.0	[146]	https://docs.anaconda.com/
cowplot 1.1.3	[147]	https://CRAN.R-project.org/package=cowplot
CytoCtrlAnalyzer	[148]	https://apps.cytoscape.org/apps/cytoctrlanalyser
Cytoscape 3.10.2	[149]	https://cytoscape.org/
Cytoscape Omnipath	[150]	https://apps.cytoscape.org/apps/omnipath
DEFormats 1.30.0	[151]	https://bioconductor.org/packages/release/bioc/html/DEFormats.html
DESeq2 1.42.1	[152]	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
edgeR 4.0.16	[153]	https://bioconductor.org/packages/release/bioc/html/edgeR.html
Enhancedvolcano 1.20.0	[154]	https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html
EnsDb.Hsapiens.v86 2.99.0	[155]	https://bioconductor.org/packages/release/data/annotation/html/EnsDb.Hsapiens.v86.html
fastp 0.23.4	[156]	https://anaconda.org/bioconda/fastp
FastQC 0.12.1	[157]	https://anaconda.org/bioconda/fastqc
ggplot2 3.5.1	[158]	https://CRAN.R-project.org/package=ggplot2
ggpubr 0.6.0	[159]	https://CRAN.R-project.org/package=ggpubr
ggraph 2.2.1	[160]	https://CRAN.R-project.org/package=ggraph
glmGamPoi 1.14.3	[161]	https://bioconductor.org/packages/release/bioc/html/glmGamPoi.html
gprofiler2 0.2.3	[162]	https://CRAN.R-project.org/package=gprofiler2
gt 0.11.0	[163]	https://CRAN.R-project.org/package=gt
igraph 2.0.3	[164]	https://CRAN.R-project.org/package=igraph
kallisto 0.50.1	[165]	https://anaconda.org/bioconda/kallisto
limma 3.58.1	[166]	https://bioconductor.org/packages/release/bioc/html/limma.html
MetBrewer 0.2.0	[167]	https://CRAN.R-project.org/package=MetBrewer
MultiQC 1.22.2	[168]	https://anaconda.org/bioconda/multiqc
OmniPathR 3.10.1	[169]	https://bioconductor.org/packages/release/bioc/html/OmnipathR.html
org.Hs.eg.db 3.18.0	[170]	https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html
pheatmap 1.0.12	[171]	https://CRAN.R-project.org/package=pheatmap
plotly 4.10.4	[172]	https://github.com/plotly/plotly.R
R 4.3.0 (2023-04-21)—“Already Tomorrow”	N/A	https://cran.r-project.org/
rhdf5 2.46.1	[173]	https://www.bioconductor.org/packages/release/bioc/html/rhdf5.html
RStudio 2024.04.2+764 (2024.04.2+764)	[174]	https://posit.co/download/rstudio-desktop/
RUVSeq 1.36.0	[175]	https://bioconductor.org/packages/release/bioc/html/RUVSeq.html
SANTA 2.38.0	[80]	https://bioconductor.org/packages/release/bioc/html/SANTA.html
tidyverse 2.0.0	[176]	https://cran.r-project.org/web/packages/tidyverse/index.html
tximport 1.30.0	[177]	https://bioconductor.org/packages/release/bioc/html/tximport.html
swamp 1.5.1	[178]	https://CRAN.R-project.org/package=swamp
Databases
Drugbank 5.0	[81]	https://go.drugbank.com/
Scripts for all the analyses can be found at https://github.com/ozgeosmanoglu/Platelet_NSCLC. All source identifiers verified on 28 October 2025.