GSVA: gene set variation analysis for microarray and RNA-seq data
10.1186/1471-2105-14-7 · doi-reference
Inferring tumour purity and stromal and immune cell admixture from expression data
10.1038/ncomms3612 · doi-reference
ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking
10.1093/bioinformatics/btq170 · doi-reference
Molecular signatures database (MSigDB) 3.0
10.1093/bioinformatics/btr260 · doi-reference
clusterProfiler: an R package for comparing biological themes among gene clusters
10.1089/omi.2011.0118 · doi-reference
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
10.1073/pnas.0506580102 · doi-reference
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
10.1038/nprot.2016.095 · doi-reference
fastp: an ultra-fast all-in-one FASTQ preprocessor
10.1093/bioinformatics/bty560 · doi-reference
Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer
10.1038/s41523-018-0066-6 · doi-reference
Pvclust: an R package for assessing the uncertainty in hierarchical clustering
10.1093/bioinformatics/btl117 · doi-reference
Mutational heterogeneity in cancer and the search for new cancer-associated genes
10.1038/nature12213 · doi-reference
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
10.1186/gb-2011-12-4-r41 · doi-reference
CNVkit: genome-wide copy number detection and visualization from targeted DNA sequencing
10.1371/journal.pcbi.1004873 · doi-reference
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
10.1093/nar/gkq603 · doi-reference
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
10.1101/gr.107524.110 · doi-reference
SomaticSniper: identification of somatic point mutations in whole genome sequencing data
10.1093/bioinformatics/btr665 · doi-reference
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing
10.1101/gr.129684.111 · doi-reference
Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs
10.1093/bioinformatics/bts271 · doi-reference
Fast and accurate short read alignment with Burrows-Wheeler transform
10.1093/bioinformatics/btp324 · doi-reference
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
10.1038/nbt.1511 · doi-reference
Multi-omics characterization of silent and productive HPV integration in cervical cancer
10.1016/j.xgen.2022.100211 · doi-reference
TPI1 activates the PI3K/AKT/mTOR signaling pathway to induce breast cancer progression by stabilizing CDCA5
10.1186/s12967-022-03370-2 · doi-reference
Targeting ferroptosis as a vulnerability in cancer
10.1038/s41568-022-00459-0 · doi-reference
Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis
10.1038/nchembio.2238 · doi-reference
Tumor-induced reshuffling of lipid composition on the endoplasmic reticulum membrane sustains macrophage survival and pro-tumorigenic activity
10.1038/s41590-021-01047-4 · doi-reference
