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UNC Lineberger

Tools

PurIST

Single-sample classifier for PDAC tumor subtypes: https://github.com/naimurashid/PurIST

Purity independent subtyping of tumors (PurIST), a clinically robust single sample classifier for tumor subtyping in pancreatic cancer. Clin Cancer Res.  2020 Jan 1;26(1):82-92. doi: 10.1158/1078-0432.CCR-19-1467. Epub 2019 Nov 21.

  • Rashid NU, Peng XL, Jin C, Moffitt RA, Volmar KE, Kawalerski R, Belt BA, Panni RZ, Nywening TM, Herrera SG, Moore KJ, Hennessey S, Morrison AB, Nayyar A, Change AE, Schmidt B, Kim HJ, Linehan DC, Yeh JJ.

DeCAF

Single-sample classifier for PDAC CAF subtypes: https://github.com/jjyeh-unc/decaf

Determination of permissive and restraining cancer-associated fibroblast (DeCAF) subtypes bioRxiv [Preprint]. 2024 May 17:2024.05.14.594197. doi: 10.1101/2024.05.14.594197.

  • Peng XL, Kharitonova EV, Xu Y, Kearney JF, Luan C, Chan PS, Hariharan A, McCabe IC, Leary JR, Morrison AB, Trembath HE, LaBella ME, Herera Loeza SG, Cliff A, Kim HJ, Belt BA, Panni RZ, Linehan DC, Damrauer JS, Iuga AC, Kim WY, Rashid NU, Yeh JJ.

DECODER

De novo deconvolution for bulk sequencing data: https://github.com/laurapeng/decoder 

Single-sample compartment weight estimation for PDAC bulk samples: https://github.com/laurapeng/decoderr

De novo compartment deconvolution and weight estimation of tumor samples using DECODER. Nat Commun. 2019 Oct 18;10(1):4729.  doi: 10.1038/s41467-019-12517-7.

  • Peng XL, Moffitt RA, Torphy RJ, Volmar KE, Yeh JJ. 

SCISSORS

Rare cell and marker gene identification for scRNAseq: https://github.com/jr-leary7/SCISSORS

Sub-Cluster Identification through Semi-Supervised Optimization of Rare-Cell Silhouettes (SCISSORS) in single-cell RNA-sequencing. Bioinformatics. 2023 Aug 1;39(8):btad449. doi: 10.1093/bioinformatics/btad449.

  • Leary JR, Xu Y, Morrison AB, Jin C, Shen EC, Kuhlers PC, Su Y, Rashid NU, Yeh JJ, Peng XL.