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2
votes
5
replies
761
views
Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
R edgeR limma RNA-seq
updated 6 months ago by 3.9k • written 6 months ago by ▴ 790
2
votes
2
replies
1.8k
views
Interpretation of functional prediction pathogenicity scores regarding variants with multiple transcripts in ANNOVAR
annovar pathogenicity cancer CADD
3.0 years ago by svlachavas ▴ 790
5
votes
5
replies
1.9k
views
How to select a "representative" transcript in multiple transcript variants from annotation with ANNOVAR and gencode
annovar gencode transcript SNP annotation
3.1 years ago by svlachavas ▴ 790
0
votes
0
replies
1.1k
views
Analyze RPPA cancer data in R for clustering patients and differential protein expression
RPPA RPPanalyzer R clustering DE
3.4 years ago by svlachavas ▴ 790
0
votes
0
replies
697
views
Filtering somatic point mutations and CNV alterations on the gene level for multi-omics data integration
feature reduction somatic mutations multiomics
3.4 years ago by svlachavas ▴ 790
2
votes
1
reply
1.3k
views
Suggested pipeline to perform variant calling for cancer exome sequencing samples of PDX models
pdx variant calling WES liquid biopsy
updated 4.0 years ago by ▴ 30 • written 4.2 years ago by ▴ 790
2
votes
3
replies
926
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R RNA-Seq DE batch-effect GTEx
updated 4 days ago by 43k • written 4.1 years ago by ▴ 790
3
votes
3
replies
1.2k
views
Suggested tool or algorithm for accessing pathogenicity and prioritization of somatic INDELs in cancer research
somatic variant annotation pathogenicity cancer
4.2 years ago by svlachavas ▴ 790
0
votes
0
replies
863
views
Suggestion of specific tools/pipelines for the manipulation and analysis of VCF files after somatic copy number variant calling
vcf cnv facets CNA VCF analysis
4.2 years ago by svlachavas ▴ 790
4
votes
6
replies
1.8k
views
Estimate tumor purity for liquid cancer biopsy samples of whole exome sequencing data
variant calling tumor purity liquid biopsy WES
updated 4.3 years ago by ▴ 100 • written 4.3 years ago by ▴ 790
0
votes
0
replies
1.1k
views
Perform correlation analysis between miRNA and mRNA expression data with different transformation values for the same samples
correlation analysis TCGA miRNA RNA-Seq
5.0 years ago by svlachavas ▴ 790
7
votes
8
replies
5.8k
views
Appropriate bed files from library capture kit for computing on target coverage of WES bam files with Picard and CollectHsMetrics
NGS WES Picard bam
updated 13 months ago by 43k • written 5.4 years ago by ▴ 790
3
votes
3
replies
1.7k
views
Group/Cluster tumor samples in an RNA-Seq dataset for survival analysis, based on the expression of a small gene signature
RNA-Seq gene signature survival clustering R
updated 5.5 years ago by 87k • written 5.6 years ago by ▴ 790
0
votes
0
replies
2.1k
views
Appropriate explanation of function resamples and diff comparing resampling distributions of 3 different training models with caret in R
caret machine learning R microarrays
updated 5.6 years ago by 20 • written 6.5 years ago by ▴ 790
6
votes
6
replies
2.5k
views
Download latest reference genome assembly for exome sequencing alignment and variant calling
reference genome dna sequence alignment
updated 5.7 years ago by 20 • written 5.8 years ago by ▴ 790
3
votes
8
replies
1.4k
views
Quality control issues for mRNA sequencing fastq files based on FastQC, based on Per Base Sequence Content
fastqc mRNAsequencing RNA-Seq sequence
updated 5.8 years ago by 47k • written 5.8 years ago by ▴ 790
4
votes
5
replies
3.7k
views
Implementation of the COSMIC database for somatic variant annotation and filtering pipeline for WES cancer data
somatic variants COSMIC variant annotation WES
5.8 years ago by svlachavas ▴ 790
8
votes
8
replies
4.5k
views
dbSNP annotation database and appropriate filtering in somatic variant calling pipelines
dbSNP variant filtering somatic variant calling
updated 5.9 years ago by 87k • written 5.9 years ago by ▴ 790
1
vote
3
replies
1.4k
views
Appropriate methodologies of comparing whole exome sequencing data between circulating tumor cells and biopsies from the same set of patients
exome sequencing variant annotation mutations
6.0 years ago by svlachavas ▴ 790
9
votes
11
replies
14k
views
Implement p-values and significance levels in boxplots for more of two groups with ggplot2 in R concerning RNA-Seq gene expression data
boxplot R RNA-Seq ggplot2
updated 2.7 years ago by 87k • written 6.1 years ago by ▴ 790
5
votes
6
replies
2.9k
views
Dissimilarity measure for computing similarity between categorical variables in R
R clustering similarity categorical features
6.1 years ago by svlachavas ▴ 790
4
votes
8
replies
2.5k
views
Appropriate creation of contigency table and impementation of fisher's exact test, for functional enrichment analysis in R
fishers exact test overepresentation analysis R
updated 6.2 years ago by 8.6k • written 6.2 years ago by ▴ 790
3
votes
9
replies
1.6k
views
Possible methodology for putative combination of different statistics and metrics for ranking of functional enrichment analysis
fishers exact test functional enrichment analysis
6.2 years ago by svlachavas ▴ 790
17
votes
26
replies
3.6k
views
Possible methodologies for association of specific gene subsets from microarray data with categorical histopathological parameters
R correlation microarrays qualitative variables
updated 6.5 years ago by 87k • written 6.5 years ago by ▴ 790
8
votes
9
replies
3.8k
views
Interpretation of GISTIC putative copy number alterations for mutations with cBioPortal in a specific cancer dataset
cBioPortal GISTIC mutations TCGA sequencing
updated 6.5 years ago by 87k • written 6.5 years ago by ▴ 790
0
votes
1
reply
3.7k
views
Clustering of gene expression data with continuous clinical quantitative parameters of different range/units
R microarray clustering clinical data
updated 7.2 years ago by 27k • written 7.2 years ago by ▴ 790
0
votes
0
replies
1.7k
views
Possible methodology-R package for simulating a microarray dataset with both gene and clinical continuous features
R microarray simulation classification
updated 7.3 years ago by 20 • written 7.4 years ago by ▴ 790
3
votes
4
replies
2.1k
views
Possible tools-programs for inspecting the relevance of DE genes to a specific cancer type
DE-genes validation microarray R Disease-Ontology
updated 21 months ago by 43k • written 8.2 years ago by ▴ 790
0
votes
0
replies
1.9k
views
Assosiation of candidate genes after drug pertubations with specific cancer type and known drug interactions
database breast cancer drug microarray genes
8.5 years ago by svlachavas ▴ 790
3
votes
8
replies
3.2k
views
Possible methodology implemented in R/Bioconductor packages to integrate and analyze clinical data with gene expression data in R
R data-integration clinical-data microarray-data
updated 19 months ago by 43k • written 8.6 years ago by ▴ 790
30 results • Page 1 of 1
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