Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient. (original) (raw)
This is a list of tools and resources that we have found mentioned in this publication.
Bioconductor (tool)
RRID:SCR_006442
Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.
BD FACSDiva Software (tool)
RRID:SCR_001456
A collection of tools for flow cytometer and application setup, data acquisition, and data analysis that help streamline flow cytometry workflows. It provides features to help users integrate flow systems into new application areas, including index sorting for stem cell and single-cell applications, as well as automation protocols for high-throughput and robotic laboratories.
UCSC Genome Browser (tool)
RRID:SCR_005780
Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data.
SAM format (tool)
RRID:SCR_012093
A generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms.
GenePattern (tool)
RRID:SCR_003201
A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.
RefSeq (tool)
RRID:SCR_003496
Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases.
Dako (tool)
RRID:SCR_013530
An Antibody supplier; Dako was purchased by Agilent in 2012 and several years later the websites began to reflect the Dako products as part of the Agilent catalog.
SAMTOOLS (software resource)
RRID:SCR_002105
Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
ABSOLUTE (software resource)
RRID:SCR_005198
Software to estimate purity / ploidy, and from that compute absolute copy-number and mutation multiplicities. When DNA is extracted from an admixed population of cancer and normal cells, the information on absolute copy number per cancer cell is lost in the mixing. The purpose of ABSOLUTE is to re-extract these data from the mixed DNA population. This process begins by generation of segmented copy number data, which is input to the ABSOLUTE algorithm together with pre-computed models of recurrent cancer karyotypes and, optionally, allelic fraction values for somatic point mutations. The output of ABSOLUTE then provides re-extracted information on the absolute cellular copy number of local DNA segments and, for point mutations, the number of mutated alleles.