Software and
Resources

Software and Resources

FFixR

FFixR

Formalin-Fixed RNA-seq artefact remover

https://github.com/yizhak-lab-ccg/FFixR

BreastScape

BreastScape

Collected and pre-processed breast cancer scRNA-seq datasets 

https://breastscape.twix.technion.ac.il/

scXpand

scXpand

T cell clonal expansion from scRNA-seq without matched TCR-seq (also part of the scverse ecosystem) 

https://github.com/yizhak-lab-ccg/scXpand

Single-cell vault

Curated and pre-processed database for paired scRNAscTCR-seq data

https://singlecellvault.net.technion.ac.il/

PRECISE

PRECISE

A machine learning-based workflow for predicting patient response to immunotherapy using scRNA-seq data

https://github.com/yizhak-lab-ccg/PRECISE-

RNA-MuTect-WMN (Without Matched-Normal)

Somatic mutation calling from RNA-seq without matched-normal samples

https://github.com/yizhak-lab-ccg/RNA_MUTECt_WMN

RNA-MuTect

Somatic mutation calling from RNA-seq

https://github.com/yizhak-lab-ccg/RNA_MUTECT_1.0

PRIME

Personalized Reconstruction of Metabolic Models

https://github.com/yizhak-lab-ccg/PRIME

MTA

Metabolic Transformation Algorithm

https://github.com/yizhak-lab-ccg/MTA

IOMA

Integrative Omics-Metabolic Analysis

https://github.com/yizhak-lab-ccg/IOMA