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566
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No baf, cn1 and cn2 columns in cnvkit call output using vcf files
BAF cnvkit Minor-cn Major-cn
2.1 years ago by rahel14350 ▴ 40
1
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1
reply
543
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Deseq2 output to ActivePathways
DeSeq2 matrix ActivePathways pathways p-value
updated 2.7 years ago by ★ 2.0k • written 2.7 years ago by ▴ 40
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1.1k
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Comment: C: ATACseq libraries differ in each run
4.4 years ago by rahel14350 ▴ 40
1
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2
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1.1k
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ATACseq libraries differ in each run
ChIP-Seq sequencing ATAC-seq
updated 17 months ago by 44k • written 4.4 years ago by ▴ 40
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2
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1.4k
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Comment: C: Correlation between gene expression (RNAseq) and RRBS methylation data
4.7 years ago by rahel14350 ▴ 40
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6
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1.4k
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Correlation between gene expression (RNAseq) and RRBS methylation data
RNA-Seq RRBS Correlation R Methylation
updated 4.7 years ago by 20k • written 4.7 years ago by ▴ 40
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1.4k
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Comment: C: Correlation between gene expression (RNAseq) and RRBS methylation data
4.7 years ago by rahel14350 ▴ 40
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0
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1.2k
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Answer: A: Enhancer identification in mm10 from RRBS data in R
4.7 years ago by rahel14350 ▴ 40
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4
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1.2k
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Enhancer identification in mm10 from RRBS data in R
R RRBS enhancer mm10 visualization
4.7 years ago by rahel14350 ▴ 40
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1
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1.2k
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Comment: C: Enhancer identification in mm10 from RRBS data in R
4.8 years ago by rahel14350 ▴ 40
3
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4
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6.6k
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converting Bed to Wig
bed WIG BigWig overlap rtracklayer
updated 5.6 years ago by 36k • written 5.6 years ago by ▴ 40
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1
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6.6k
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Comment: C: converting Bed to Wig
5.6 years ago by rahel14350 ▴ 40
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3
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4.3k
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Applying machine learning algorithms on RNAseq data using R
RNAseq MLSeq machine learning SVM RF
5.7 years ago by rahel14350 ▴ 40
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1
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4.3k
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Comment: C: Applying machine learning algorithms on RNAseq data using MLSeq package or other
5.7 years ago by rahel14350 ▴ 40
2
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2
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1.6k
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Percentages of samples mutated in individual tumour
Maftool GenVisR SNP frequency SNP percentage
updated 5.7 years ago by 20 • written 8.0 years ago by ▴ 40
1
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4
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2.4k
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R packages for applying Data mining or machine learning algorithms (SNV,RF, Neural Network) on RNAseq data
RNA-Seq Data minning Machine Learning R packages
5.8 years ago by rahel14350 ▴ 40
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0
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2.4k
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Comment: C: R packages for Data mining or machine learning of a set of differentialy express
5.8 years ago by rahel14350 ▴ 40
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0
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2.4k
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Comment: C: R packages for Data mining or machine learning of a set of differentialy express
5.8 years ago by rahel14350 ▴ 40
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0
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1.6k
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Comment: C: count tables from RNA-seq data on GEOmetadb
6.3 years ago by rahel14350 ▴ 40
2
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2
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1.6k
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count tables from RNA-seq data on GEOmetadb
GEOmetadb RNA-Seq GEOquery SRAdb GEO
updated 6.3 years ago by 27k • written 6.3 years ago by ▴ 40
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0
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3.4k
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Comment: C: Differentially methylated regions (DMRs) and sites (DMCs) are not in the same re
6.4 years ago by rahel14350 ▴ 40
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0
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3.4k
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Comment: C: Differentially methylated regions (DMRs) and sites (DMCs) are not in the same re
6.4 years ago by rahel14350 ▴ 40
6
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4
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3.4k
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Differentially methylated regions (DMRs) and sites (DMCs) are not in the same region
RRBS RnBeads Metilene Methylkit
updated 6.5 years ago by 104k • written 6.5 years ago by ▴ 40
1
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12
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2.2k
views
error in using LOLA enrichment analysis in RnBeads
RnBeads LOLA Enrichment RRBS
updated 6.5 years ago by 47k • written 6.5 years ago by ▴ 40
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0
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2.2k
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Comment: C: error in using LOLA enrichment analysis in RnBeads
6.5 years ago by rahel14350 ▴ 40
0
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1
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2.2k
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Comment: C: error in using LOLA enrichment analysis in RnBeads
6.5 years ago by rahel14350 ▴ 40
0
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1
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2.2k
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Comment: C: error in using LOLA enrichment analysis in RnBeads
6.5 years ago by rahel14350 ▴ 40
0
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1
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2.2k
views
Comment: C: error in using LOLA enrichment analysis in RnBeads
6.5 years ago by rahel14350 ▴ 40
0
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2
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2.2k
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Comment: C: error in using LOLA enrichment analysis in RnBeads
updated 6.5 years ago by 47k • written 6.5 years ago by ▴ 40
1
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0
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2.2k
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Comment: C: annotation of RRBS DMRs in RnBeads or other packages
6.9 years ago by rahel14350 ▴ 40
1
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1
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2.2k
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annotation of RRBS DMRs in RnBeads or other packages
RRBS DMRs RnBeads annotation Granges
6.9 years ago by rahel14350 ▴ 40
0
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0
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2.6k
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filtering (deleting) the overlapped genomic ranges from two GRangelist using findOverlaps
findOverlap GenomicRanges overlapped
7.1 years ago by rahel14350 ▴ 40
0
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0
replies
1.8k
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KNIME workflow for data mining of protein expression data from TCGA
KNIME Data mining Protein TCGA Biomarker
7.3 years ago by rahel14350 ▴ 40
0
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0
replies
1.7k
views
missing values for beta values in Rnbeads (imputation of NAs)
RnBeads NA Beta values Methylation values
7.3 years ago by rahel14350 ▴ 40
1
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0
replies
3.5k
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Answer: A: categorize DMRs by type (hyper - hypo methilated) in DMRcate or minfi
7.3 years ago by rahel14350 ▴ 40
1
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1
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3.5k
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categorize DMRs by type (hyper - hypo methilated) in DMRcate or minfi
DMRcate minfi Hyper methylated Hypo mehylated 450k
7.3 years ago by rahel14350 ▴ 40
0
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1
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1.9k
views
Comment: C: deconvolution of heterogenous cell types in RRBS data
7.3 years ago by rahel14350 ▴ 40
2
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3
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1.9k
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deconvolution of heterogenous cell types in RRBS data
RRBS deconvolution methylome
7.3 years ago by rahel14350 ▴ 40
0
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0
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1.7k
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Answer: Answer: RRBS data analysis using RnBeads give Scan() error
updated 7 months ago by 44k • written 7.3 years ago by ▴ 40
0
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1
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1.7k
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RRBS data analysis using RnBeads give Scan() error
RRBS 450k RnBeads
updated 7 months ago by 44k • written 7.3 years ago by ▴ 40
0
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0
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2.4k
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Comment: C: biomarkers identification by data mining of public genomic tumour databases in R
7.4 years ago by rahel14350 ▴ 40
1
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4
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2.4k
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biomarkers identification by data mining of public genomic tumour databases in R or Python
Data mining R TCGA biomarker python
updated 7.4 years ago by • 0 • written 7.4 years ago by ▴ 40
0
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0
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2.4k
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Comment: C: Data mining of bio-medical databases in R
7.4 years ago by rahel14350 ▴ 40
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0
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2.7k
views
Comment: C: visualization of DMRcate or minfi output on UCSC
7.5 years ago by rahel14350 ▴ 40
0
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1
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2.7k
views
Comment: C: visualization of DMRcate or minfi output on UCSC
7.5 years ago by rahel14350 ▴ 40
0
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1
reply
2.7k
views
Comment: C: visualization of DMRcate or minfi output on UCSC
7.5 years ago by rahel14350 ▴ 40
3
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6
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2.7k
views
visualization of DMRcate or minfi output on UCSC
DMRcate minfi 450k Track hub UCSC
updated 7.5 years ago by ▴ 130 • written 7.5 years ago by ▴ 40
0
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0
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3.0k
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Comment: C: how to do noob+funnorm+bmiq normalization together in minfi or RnBeads?
7.6 years ago by rahel14350 ▴ 40
1
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3
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3.0k
views
how to do noob+funnorm+bmiq normalization together in minfi or RnBeads?
minfi RnBeads preprocessFunnorm BMIQ 450k
7.6 years ago by rahel14350 ▴ 40
0
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0
replies
2.1k
views
Correcting batch effect from known variables in RnBeads using Combat
Combat 450k methylation RnBeads batch-effect
updated 7 months ago by 44k • written 7.7 years ago by ▴ 40
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