Appendix E — Citation

Guidelines

If OSTA has been useful to your research, please consider citing:

HL Crowell*°, Y Dong*, I Billato, P Cai, M Emons, S Gunz, B Guo, M Li, A Mahmoud, A Manukyan, H Pagès, P Panwar, S Rao, CJ Sargeant, L Shepherd Kern, M Ramos, J Sun, M Totty, VJ Carey, Y Chen, L Collado-Torres, S Ghazanfar, KD Hansen, K Martinowich, KR Maynard, E Patrick, D Righelli, D Risso, S Tiberi, L Waldron, R Gottardo†°, MD Robinson†°, SC Hicks†°, LM Weber†°. Orchestrating spatial transcriptomics analysis with Bioconductor. bioRxiv (2025). DOI: 10.1101/2025.11.20.688607

(* co-first. † co-senior. ° correspondence.)

Notably, OSTA pieces together work and information from numerous researchers. As such, we suggest readers cite the pieces of work they have either used or consulted to conduct their research – be it (R, Python, or other) software, benchmarks that informed their methodological decisions, review or perspective pieces, or other. To facilitate this, we provide a list in the section below.

Collection

We here make an attempt to collect all biotechnology, dataset, software, review, benchmark, or other, references and resources mentioned throughout the book.

If you spot any obvious omissions or mistakes, please let us know!
Bioconductor Gentleman et al. (2004); Huber et al. (2015); Carey (2025)
OSCA Amezquita et al. (2020)
benchmark Hartman and Satija (2024)
CosMx He et al. (2022)
Curio Seeker Curio Bioscience
MERFISH Chen et al. (2015)
MERSCOPE Vizgen
Slide-seqV2 Stickels et al. (2021)
ST Ståhl et al. (2016)
Stereo-seq STOmics
Visium 10x Genomics
Visium HD 10x Genomics
Xenium 10x Genomics
3D ST Vickovic et al. (2022)
Open-ST Schott et al. (2024); Schott et al. (2025)
PASTE Zeira et al. (2022)
PASTE2 X. Liu et al. (2023)
STalign Clifton et al. (2023)
STARmap Wang et al. (2018)
Deep-STARmap Sui et al. (2025)
3D MERFISH Fang et al. (2024)
C3PO Cotterell et al. (2024)
CLARITY Tomer et al. (2014)
3DISCO Ertürk et al. (2012)
DISCO-MS Bhatia et al. (2022)
sc4D Rao et al. (2025)
MOSAICA Vu et al. (2022)
scMAGS Baran and Doğan (2023)
CITE-seq Y. Liu et al. (2023)
spatial omics Moffitt et al. (2022); Bressan et al. (2023)
spatial analyses Palla, Fischer, et al. (2022)
spatial proteomics Semba and Ishimoto (2024); Lundberg and Borner (2019)
spatial epigenomics D. Zhang et al. (2023)
spatial transcriptomics Rao et al. (2021); Moses and Pachter (2022); Cheng et al. (2023); Tian et al. (2023)
single-cell spatial proteomics Paul et al. (2021); Mund et al. (2022)
single-cell & spatial transcriptomics Gulati et al. (2025)
probe selection & panel design Kuemmerle et al. (2024); Y. Zhang et al. (2024)
mass spectrometry imaging H. Zhang et al. (2024); Palomino and Muddiman (2025)
sf Pebesma (2018)
sp Pebesma and Bivand (2005)
Rarr Smith and Gruson (2023)
pizzarr n/a
alabaster.base Lun (2023)
MoleculeExperiment Peters Couto et al. (2023)
SingleCellExperiment Amezquita et al. (2020)
SpatialExperiment Righelli et al. (2022)
SpatialFeatureExperiment Moses et al. (2023)
Seurat Hao et al. (2023)
Scanpy Wolf et al. (2018)
Squidpy Palla, Spitzer, et al. (2022)
Giotto J. G. Chen et al. (2025); Dries et al. (2021)
VoltRon Manukyan et al. (2023)
spatialGE Ospina et al. (2022)
SpatialData Marconato et al. (2025)
Bruker’s CosMx AtoMx
Vizgen’s MERSCOPE Visualizer
10 Genomic’s Xenium Xenium Explorer
10 Genomic’s Visium Loupe Browser
Seurat-Loupe conversion loupeR
iSEE Rue-Albrecht et al. (2018)
napari Sofroniew et al. (2025)
BiocPkgTools Su et al. (2025)
BiocViews Carey et al. (2025)
10x Genomics’ Visium processing Space Ranger
10x Genomics’ Xenium processing Xenium Ranger
Bruker’s CosMx processing AtoMx
Bruker’s CosMx tutorials scratch space
SpatialExperimentIO
SpatialFeatureExperiment Moses et al. (2023)
VisiumIO
XeniumIO
human breast cancer (Visium, Xenium) Janesick et al. (2023)
colorectal carcinoma (Visium/HD, Xenium) de Oliveira et al. (2025)
mouse brain (1k-plex CosMx) Bruker
human brain (6k-plex CosMx) Bruker
human brain (Visium) Maynard et al. (2021)
type I diabetes (IMC) Damond et al. (2019)
axolotl brain (Stereo-seq) Wei et al. (2022)
spatialLIBD Pardo et al. (2022)
STexampleData Righelli et al. (2022)
anndata` Virshup et al. (2024)
anndataR Deconinck et al. (2026)
basilisk Lun (2022)
reticulate Ushey et al. (2017)
zellkonverter Zappia et al. (2020)
technical publishing systems R Markdown, Quarto
Rsubread Liao et al. (2019)
stPipe Xu et al. (2025)
10x Genomics’ Visium SpaceRanger
STOmics’ Stereo-seq SAW; Gong et al. (2024)
theory Bhuva et al. (2024)
scrapper
scater McCarthy et al. (2017)
SpotSweeper Totty et al. (2025)
SpaceTrooper Banzi et al. (2025)
CARDspa Ma and Zhou (2022)
cell2location Kleshchevnikov et al. (2022)
DSTG Song and Su (2021)
NMFreg_tutorial
novosparc Nitzan et al. (2019)
Giotto’s SpatialDWLS J. G. Chen et al. (2025)
scvi-tools’s DestVI Lopez et al. (2022)
SD2 H. Li et al. (2022)
spacexr’s RCTD Cable, Murray, Zou, et al. (2022)
SpaOTsc Cang and Nie (2020)
SpatialDecon Danaher et al. (2022)
SpiceMIx Chidester et al. (2023)
SPOTlight Elosua-Bayes et al. (2021)
std-poisson Berglund et al. (2018)
STdeconvolve Miller et al. (2022)
stereoscope Andersson et al. (2020)
STRIDE Sun et al. (2022)
Tangram Biancalani et al. (2021)
benchmarks Sang-aram et al. (2023); H. Li et al. (2023); Gaspard-Boulinc et al. (2025)
bin2cell)) Polański et al. (2024)
stardist Weigert and Schmidt (2022)
SMURF Guo et al. (2025)
SpaceRanger v4 10x Genomics
Sanofi’s ENACT pipeline Kamel et al. (2025)
Baysor Petukhov et al. (2022)
cellpose Stringer et al. (2021)
proseg Jones et al. (2025)
ssam Park et al. (2021)
SPLIT Bilous et al. (2025)
cellAdmix Mitchel et al. (2026)
segger_dev Heidari et al. (2025)
FastReseg Wu et al. (2024)
hoodscanR Liu et al. (2025)
imcRtools Windhager et al. (2023)
scider Li et al. (2025)
limma Baldoni et al. (2025)
edgeR Y. Chen et al. (2025)
DeepST Xu et al. (2022)
GraphST Long et al. (2023)
NicheCompass Birk et al. (2025)
Novae Blampey et al. (2025)
SpaGCN Hu et al. (2021)
STAGATE Dong and Zhang (2022)
review Behanova et al. (2022), Summers et al. (2022)
CCPlotR Ennis et al. (2023)
CellChatDB Jin et al. (2021)
CellphoneDB Efremova et al. (2020)
COMMOT Cang et al. (2023)
Giotto J. G. Chen et al. (2025)
mistyR Tanevski et al. (2022)
SpaOTsc Cang and Nie (2020)
SpatialDM Zhuoxuan Li et al. (2023)
theory Oyler-Yaniv et al. (2017)
review Armingol et al. (2020)
benchmark Liu et al. (2022)
theory Cassella and Ephrussi (2022)
Visium HD Novoselsky et al. (2026)
Bento Mah et al. (2024)
MoleculeExperiment Peters Couto et al. (2023)
FISHFactor Walter et al. (2023)
ClusterMap He et al. (2021)
CellSP Aggarwal and Sinha (2025)
MAGIC Dijk et al. (2018)
Tangram Biancalani et al. (2021)
InSTAnT (Kumar2024-Instant?)
SPRAWL Bierman et al. (2024)
SpaGNN Fang et al. (2023)
scrapper
scater McCarthy et al. (2017)
SpaNorm Salim et al. (2025)
theory Bhuva et al. (2024); Atta et al. (2024)
bulk vs. scRNA-seq Vallejos et al. (2017)
scRNA-seq benchmark Ahlmann-Eltze and Huber (2023)
quick tips Nguyen and Holmes (2019)
perspective Chari and Pachter (2023)
benchmarks Xiang et al. (2021); Pandit et al. (2022)
BANKSY Singhal et al. (2024)
BayesSpace Zhao et al. (2021)
CellCharter Varrone et al. (2024)
Leiden Traag et al. (2019)
PRECAST W. Liu et al. (2023)
PROST Liang et al. (2024)
SpaceFlow Ren et al. (2022)
STAGATE Dong and Zhang (2022)
CellAssign Zhang et al. (2019)
scType Ianevski et al. (2022)
SingleR Aran et al. (2019)
azimuth Hao et al. (2021)
scvi-tools’s scANVI (Xu et al. 2021)
celltypist Domínguez Conde et al. (2022)
scFoundation Hao et al. (2024)
scGPT Cui et al. (2024)
Geneformer Theodoris et al. (2023)
HCA Regev et al. (2017)
Tabula Sapiens Tabula Sapiens Consortium* et al. (2022)
Tabula Muris Tabula Muris Consortium et al. (2018)
Tabula Muris Senis Tabula Muris Consortium (2020)
SAHA Park et al. (2025)
CELLxGENE Megill et al. (2021)
HPA Thul and Lindskog (2018)
scDiagnostics Christidis et al. (2026)
review Wang et al. (2024)
benchmarks R. Chen et al. (2025); Sun et al. (2025)
Cheng et al. (2022); Hu et al. (2024)
T. Liu et al. (2024); Xiong et al. (2025)
C-SIDE Cable, Murray, Shanmugam, et al. (2022)
CTSV Yu and Luo (2022)
DESpace Cai et al. (2024)
nnSVG Weber et al. (2023)
scran Lun et al. (2016)
SPARK Sun et al. (2020); Zhu et al. (2021)
spatialDE Svensson et al. (2018)
spVC Yu and Li (2024)
reviews Adhikari et al. (2024); Yan et al. (2024)
benchmarks Zhijian Li et al. (2023); Chen et al. (2024)
msigdb n/a
msigdbr n/a
AUCell Aibar et al. (2017)
Molecular Signatures Database (MSigDB) Subramanian et al. (2005)
pasta Emons et al. (2025)
spatstat Baddeley and Turner (2005)
1st law of geography Tobler (1970)
spatial analysis Dale and Fortin (2014)
spatial data science Pebesma and Bivand (2023)
point pattern analysis Baddeley et al. (2015)
Lee’s L Lee (2001)
Ripley’s K Ripley (1976)
LISA metric Anselin (1995); Anselin (2019)
joint count statistics Getis (2009)
napari Sofroniew et al. (2025)
QuPath Bankhead et al. (2017)
Prov-GigaPath Xu et al. (2024)
The Cancer Genome Atlas (TCGA) Tomczak et al. (2015)
The Cancer Imaging Archive (TCIA) n/a
imageTCGA n/a
TCIAAPI n/a
C-SIDE Cable, Murray, Shanmugam, et al. (2022)
DESpace Cai et al. (2024)
lme4 Bates et al. (2015)
lmerTest Kuznetsova et al. (2017)
sosta Gunz et al. (2025)
spatialFDA Emons et al. (2026)
spicyR Canete et al. (2022)
silhouette width Rautenstrauch and Ohler (2025)
harmony Korsunsky et al. (2019)
CellMixS Lütge et al. (2021)
rliger Welch et al. (2019)
scvi-tool’s Tangram Biancalani et al. (2021)
SLAT Xia et al. (2023)
CeLEry Q. Zhang et al. (2023)
novosparc Nitzan et al. (2019)
SpaOTsc Cang and Nie (2020)
imputation benchmark B. Li et al. (2022)
integration review Argelaguet et al. (2021)
integration benchmarks Tran et al. (2020); Chazarra-Gil et al. (2021); Luecken et al. (2022)
registration benchmark Hu et al. (2024); Dong et al. (2025); Yan et al. (2026)
registration challenge Weitz et al. (2024)
infercnv n/a
infercnvpy n/a
CNV benchmarks Jensen et al. (2025); Schmid et al. (2025)
monocle Trapnell et al. (2014); Qiu et al. (2017)
slingshot Street et al. (2018)
SpaceFlow Ren et al. (2022)
stlearn Pham et al. (2023)
spaTrack Shen et al. (2025)
trajectory benchmarks Cannoodt et al. (2016); Saelens et al. (2019)
scGPT Cui et al. (2024)
scFoundation Hao et al. (2024)
Geneformer Theodoris et al. (2023)
Prov-GigaPath Xu et al. (2024)
FM review Szałata et al. (2024); Ahlmann-Eltze et al. (2026)
annotation benchmark Kedzierska et al. (2025)
perturbation prediction benchmark Ahlmann-Eltze et al. (2025)
spatial multi-omics review Vandereyken et al. (2023); X. Liu et al. (2024); Isik et al. (2026)
MOFA2 Velten et al. (2022)
MultiAssayExperiment n/a
SpatialGlue Long et al. (2024)
scvi-tool’s MultiVI Ashuach et al. (2023)

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