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Showing :
questions
2
votes
5
replies
795
views
Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
R
edgeR
limma
RNA-seq
updated 7 months ago by
LChart
3.9k • written 7 months ago by
svlachavas
▴ 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
3.1 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
3.2 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
3.5 years ago by
svlachavas
▴ 790
0
votes
0
replies
706
views
Filtering somatic point mutations and CNV alterations on the gene level for multi-omics data integration
feature reduction
somatic mutations
multiomics
3.5 years ago by
svlachavas
▴ 790
2
votes
1
reply
1.4k
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
akshayb04
▴ 30 • written 4.3 years ago by
svlachavas
▴ 790
2
votes
3
replies
942
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 25 days ago by
Ram
43k • written 4.1 years ago by
svlachavas
▴ 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
877
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
4.3 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
amjad
▴ 100 • written 4.4 years ago by
svlachavas
▴ 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
5.1 years ago by
svlachavas
▴ 790
7
votes
8
replies
5.9k
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
Ram
43k • written 5.4 years ago by
svlachavas
▴ 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 5.6 years ago by
Kevin Blighe
87k • written 5.6 years ago by
svlachavas
▴ 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 5.7 years ago by
Biostar
20 • written 6.5 years ago by
svlachavas
▴ 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 5.8 years ago by
Biostar
20 • written 5.9 years ago by
svlachavas
▴ 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
WouterDeCoster
47k • written 5.8 years ago by
svlachavas
▴ 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
5.9 years ago by
svlachavas
▴ 790
8
votes
8
replies
4.6k
views
dbSNP annotation database and appropriate filtering in somatic variant calling pipelines
dbSNP
variant filtering
somatic variant calling
updated 5.9 years ago by
Kevin Blighe
87k • written 5.9 years ago by
svlachavas
▴ 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
6.1 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 2.8 years ago by
Kevin Blighe
87k • written 6.1 years ago by
svlachavas
▴ 790
5
votes
6
replies
3.0k
views
Dissimilarity measure for computing similarity between categorical variables in R
R
clustering
similarity
categorical features
6.2 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
Carlo Yague
8.7k • written 6.2 years ago by
svlachavas
▴ 790
3
votes
9
replies
1.7k
views
Possible methodology for putative combination of different statistics and metrics for ranking of functional enrichment analysis
fishers exact test
functional enrichment analysis
6.3 years ago by
svlachavas
▴ 790
17
votes
26
replies
3.7k
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
Kevin Blighe
87k • written 6.6 years ago by
svlachavas
▴ 790
8
votes
9
replies
3.9k
views
Interpretation of GISTIC putative copy number alterations for mutations with cBioPortal in a specific cancer dataset
cBioPortal
GISTIC
mutations
TCGA
sequencing
updated 6.6 years ago by
Kevin Blighe
87k • written 6.6 years ago by
svlachavas
▴ 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 7.3 years ago by
Jean-Karim Heriche
27k • written 7.3 years ago by
svlachavas
▴ 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
Biostar
20 • written 7.4 years ago by
svlachavas
▴ 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
Ram
43k • written 8.3 years ago by
svlachavas
▴ 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
3.3k
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 20 months ago by
Ram
43k • written 8.7 years ago by
svlachavas
▴ 790
30 results • Page
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