Historical perspective and future directions: computational science in immuno-oncology.

"table 2 single-cell rna sequencing methods method general purpose code availability reference metaneighbor cell type annotation https://github com/maggiecrow/metaneighbor cellassign cell type annotation https://github com/irrationone/cellassign garnett cell type annotation https://cole-trapnell-lab github io/garnett/ spectra cell type and gene program annotation https://github com/dpeerlab/spectra/ vision gene signature scoring https://github com/yoseflab/vision monocle pseudotime analysis http://cole-trapnell-lab github io/monocle-release/ tscan pseudotime analysis https://github com/zji90/tscan paga pseudotime analysis https://github com/theislab/paga cellphonedb cell-cell communication https://github com/teichlab/cellphonedb cellchat cell-cell communication https://github com/sqjin/cellchat nichenet cell-cell communication https://github com/saeyslab/nichenetr multinichenet cell-cell communication https://github com/saeyslab/multinichenetr merfish spatial transcriptomics https://github com/zhuanglab/merfish_analysis seqfish+ spatial transcriptomics https://github com/caigroup/seqfish-plus starmap spatial transcriptomics https://github com/weallen/starmap scater scrna-seq pipeline http://bioconductor org/packages/scater seurat scrna-seq pipeline https://github com/satijalab/seurat scanpy scrna-seq pipeline https://github com/theislab/scanpy scenic+ multiomic analysis (scatac-seq and scrna-seq) pipeline https://scenicplus readthedocs io/en/latest/ cytosig cytokine signaling level estimation https://github com/data2intelligence/cytosig/ infercnv cnv estimation https://github com/broadinstitute/infercnv copykat cnv estimation https://github com/navinlabcode/copykat scevan cnv estimation https://github com/antoniodefalco/scevan scatac-seq single-cell sequencing assay for transposase-accessible chromatin; scrna-seq single-cell rna sequencing the composition and functional state of cells within the tme continuously evolves due to cellular cues and oncogenic signaling from progressing tumors creating another layer of complexity in disease modeling. downstream filtering and processing of tcr and bcr sequences have previously been reviewed 10 1136/jitc-2023-008306 supp1 supplementary data table 3 immune cell receptor reconstruction methods method name cell type sequencing code availability reference trust4 b and t cell bulk rna-seq and scrna-seq https://bitbucket org/liulab/trust mixcr b and t cell bulk rna-seq and scrna-seq https://mixcr readthedocs io imrep b and t cell bulk rna-seq https://github com/mangul-lab-usc/imrep catt t cell bulk rna-seq and scrna-seq https://github com/guobioinfolab/catt v'djer b cell bulk rna-seq and scrna-seq https://github com/mozack/vdjer tracer t cell scrna-seq https://github com/teichlab/trace trapes t cell scrna-seq https://github com/yoseflab/trapes sctcrseq t cell scrna-seq https://github com/elementolab/sctcrseq bracer b cell scrna-seq https://github com/teichlab/bracer baldr b cell scrna-seq https://github com/bosingerlab/baldr basic b and t cell scrna-seq https://github com/akds/basic vdjpuzzle b and t cell scrna-seq https://github com/simone-rizzetto/vdjpuzzle rna-seq rna sequencing; scrna-seq single-cell rna sequencing with the frequency and sequences of t and b cell receptor chains found from immune cell reconstruction methods t and b cell population dynamics can be inferred and used for therapeutic strategies."

"Competing interests: CAR and KM declare no conflicts of interest. EMVA disclosures: Advisory/consulting: Tango Therapeutics, Genome Medical, Genomic Life, Enara Bio, Manifold Bio, Monte Rosa, Novartis Institute for Biomedical Research, Riva Therapeutics, Serinus Bio. Research support: Novartis, Bristol-Myers Squibb, Sanofi. Equity: Tango Therapeutics, Genome Medical, Genomic Life, Syapse, Enara Bio, Manifold Bio, Microsoft, Monte Rosa, Riva Therapeutics, Serinus Bio. Travel reimbursement: None. Patents: Institutional patents filed on chromatin mutations and immunotherapy response, and methods for clinical interpretation; intermittent legal consulting on patents for Foaley & Hoag."

"Funding: The authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors."