Data files

Aligned sequencing data is available in the NCBI Sequence Read Archive (SRA, https://www.ncbi.nlm.nih.gov/sra/) under accession SRP095082. Variants were called using GATK HaplotypeCaller (version 3.6). After joint performing joint genotyping multi-sample vcf file was generated. Next, SNPs and indels were extracted into two different vcf files and specific set of filters were applied for each case.

This is the submission accompanying raw result files for multiple-layer SOM (ml-SOM) analysis for the paper "Transcriptome patterns of BRCA1- and BRCA2- mutated breast and ovarian cancers".

The dataset contains the results of the ml-SOM analysis of RNA-sequencing data from TCGA-OV (ovarian cancer) and TCGA-BRCA (breast cancer) projects.

The dataset is organized as follows:

Folder "12.BC.40 - Results" - ml-SOM analysis of TCGA-BRCA (breast cancer) dataset Folder "12.OV.40 - Results" - ml-SOM ...

oposSOM is a comprehensive data analysis software combining diversity analyses, biomarker selection, functional information mining, and visualization to the machine learning based ‘high-dimensional data portraying’.

Single-cell RNA sequencing of residual cells from 24 CAR T-cell infusion products.

nuc_ctDNA_process ImageJ 1.x macros and Matlab code for processing 3D nuclear classification and quantification. This repo is designed to help you recreate the methods use in the associated publication. Please don't hesitate to contact if you have questions. Happy to debug, update, etc if there's need.

Lif files: Use ImageJ 1.x macro in fiji folder to process lif files for subsequent ilastik and Matlab processing. Works with 3 channel data (DAPI, DIC, Rh-Red-X) and 4 channel data (DAPI, Cy5, ...