Cancer Genomics and Systems Biology Laboratory

Resources and Software

Neighborseq - Software to identify and annotate the architecture of direct cell-cell interactions and relevant ligand-receptor signaling from the undissociated cell fractions in massively parallel single cell sequencing data. Software availability: https://github.com/sjdlabgroup/Neighborseq

Reference: Ghaddar B, De S. (2020) Reconstructing physical cell interaction networks from single-cell data using Neighbor-seq. Nucleic Acids Res (in press)


SAHMI - An R resource for analyzing tumor-associated microbiome at single cell level. Software availability: https://github.com/sjdlabgroup/SAHMI

Reference: Ghaddar B et al. Tumor-microbiome links subtype, cellular programs, and immunity in pancreatic cancer. (submitted)


MutSigTools - An R resource for analyzing somatic mutational signatures in cancer genomes. Software availability: https://github.com/sjdlabgroup/MutSigTools

Reference: Singh VK, Rastogi A, Hu X, Wang Y, De S. (2020) Mutational signature SBS8 predominantly arises due to late replication errors in cancer. Commun Biol. 3(1):421. PMID: 32747711


MetaITH - An R resource for estimating multi-dimensional intr-tumor heterogeneity including at the levels of genetic, transcriptomic, and immune-signatures. Software availability: https://github.com/sjdlabgroup/metaITH/

Reference: Sharma A, Merritt E, Hu X, Cruz A, Jiang C, Sarkodie H, Zhou Z, Malhotra J, Riedlinger GM, De S. (2019) Non-Genetic Intra-Tumor Heterogeneity Is a Major Predictor of Phenotypic Heterogeneity and Ongoing Evolutionary Dynamics in Lung Tumors. Cell Rep. 29(8):2164-2174.e5. PMID: 31747591.


SomVarIUS - A computational method for detecting somatic variants using high throughput sequencing data from unpaired tissue samples. Software availability: https://github.com/kylessmith/SomVarIUS

Reference: Smith KS, Yadav VK, Pei S, Pollyea DA, Jordan CT, De S. (2016) SomVarIUS: Somatic variant identification from unpaired tissue samples. Bioinformatics. [Epub ahead of print] PMID: 26589277.


SASE-hunter - Software for identifying signature of accelerated somatic evolution marked by a significant excess of somatic mutations localized in a genomic locus, and prioritized those loci that carried the signature in multiple cancer patients. Software availability: https://github.com/kylessmith/SASE-hunter

Reference: Smith KS, Yadav VK, Pedersen BS, Shaknovich RS, Geraci MW, Pollard KS, De S. (2015) Signatures of accelerated somatic evolution in gene promoters in multiple cancer types. Nucleic Acids Res 43(11):5307-17. PMID: 25934800


CruzDB - Software for annotation of genomic intervals with UCSC genome-browser database without resorting to awk-ful, error-prone manipulations. Software availability: https://github.com/brentp/cruzdb

Reference: Pedersen BS, Yang IV, De S. (2013) CruzDB: software for annotation of genomic intervals with UCSC genome-browser database. Bioinformatics. 29(23):3003-6. PMID: 24037212