svlachavas • 770
Status: New
Handle: @svlachavas-7225
Reputation: 770
Joined: 6.0 years ago
Last seen: 5 days ago
Location: Germany/Heidelberg/German Cancer Research Center

Post-doc/Guest scientist at the German Cancer Research Center (DKFZ) in the department of Medical Informatics in Translational Oncology (MITRO). 

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Comment: Comment: Issues with installation status of R package rtracklayer
12 days ago
svlachavas • 770
3
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Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
13 days ago • updated 12 days ago
svlachavas • 770
3
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4
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167
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Error with R package curatedTCGAData while trying to download TCGA MultiAssayExperiments
MultiAssayExperiment curatedTCGAData TCGAutils
5 weeks ago
svlachavas • 770
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Comment: Comment: Error with R package curatedTCGAData while trying to download TCGA MultiAssayExp
5 weeks ago
svlachavas • 770
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167
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Comment: Comment: Error with R package curatedTCGAData while trying to download TCGA MultiAssayExp
5 weeks ago
svlachavas • 770
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125
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Error in MAE experiment regarding the replacement of internal assays with different number of features
MultiAssayExperiment curatedTCGAData TCGAutils
6 weeks ago
svlachavas • 770 • updated 6 weeks ago
Marcel Ramos 490
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125
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Comment: Comment: Error in MAE experiment regarding the replacement of internal assays with differ
6 weeks ago
svlachavas • 770
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227
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Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
7 weeks ago • updated 6 weeks ago
svlachavas • 770
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227
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Comment: Comment: Transformation of raw RSEM gene expression estimates with variance stabilizing t
6 weeks ago
svlachavas • 770
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227
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Comment: Comment: Transformation of raw RSEM gene expression estimates with variance stabilizing t
6 weeks ago
svlachavas • 770
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1
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227
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Comment: Comment: Transformation of raw RSEM gene expression estimates with variance stabilizing t
7 weeks ago
svlachavas • 770
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96
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Comment: C: Converstion of Ranged Summarized Experiment to Data Frame
3 months ago
svlachavas • 770
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207
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Comment: C: Implementation of MultiAssayExperiment and curatedTCGAData R packages for querin
3 months ago
svlachavas • 770
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207
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Implementation of MultiAssayExperiment and curatedTCGAData R packages for quering and prosessing multi-omics cancer datasets
MultiAssayExperiment curatedTCGAData TCGAutils
3 months ago
svlachavas • 770 • updated 6 weeks ago
Marcel Ramos 490
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96
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Answer: A: Converstion of Ranged Summarized Experiment to Data Frame
3 months ago
svlachavas • 770
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63
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Interpretation of mroast p-value results for gene set testing of specific molecular signatures using microarray data
mroast camera gene set testing
3 months ago
svlachavas • 770
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207
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Comment: C: Possible batch effect correction with RNA-Seq data when the batches do not conta
9 months ago
svlachavas • 770
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207
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Comment: C: Possible batch effect correction with RNA-Seq data when the batches do not conta
9 months ago
svlachavas • 770
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207
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Possible batch effect correction with RNA-Seq data when the batches do not contain both biological conditions for DE analysis
batch effect limma rna seq DE
9 months ago
svlachavas • 770 • updated 9 months ago
Steve Lianoglou 13k
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110
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Comment: C: How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package
9 months ago
svlachavas • 770
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110
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Comment: C: How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package
9 months ago
svlachavas • 770
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5
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110
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How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq rna-seq filtering DE deseq2
9 months ago
svlachavas • 770 • updated 9 months ago
Michael Love 31k
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118
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Comment: C: Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays f
9 months ago
svlachavas • 770
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118
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Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
9 months ago
svlachavas • 770 • updated 9 months ago
James W. MacDonald 55k
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118
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Comment: C: Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays f
9 months ago
svlachavas • 770
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98
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Answer: A: Joint pathway Analysis using both gene and metabolite data sets
10 months ago
svlachavas • 770
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100
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Comment: C: Weird error in Rstudio trying to retreive and load genomic data from external da
10 months ago
svlachavas • 770
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100
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Comment: C: Weird error in Rstudio trying to retreive and load genomic data from external da
10 months ago
svlachavas • 770
1
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4
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100
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Weird error in Rstudio trying to retreive and load genomic data from external databases
R software error Bioconductor
10 months ago
svlachavas • 770
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1
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117
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Comment: C: Difference in dimensionality reduction plots based on DESeq2 R package and core
11 months ago
svlachavas • 770
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1
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117
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Comment: C: Difference in dimensionality reduction plots based on DESeq2 R package and core
11 months ago
svlachavas • 770
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117
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Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
11 months ago
svlachavas • 770
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378
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Comment: C: Apply different cutoffs with edgeR pipeline and glmTreat for RNA-Seq DEG analysi
11 months ago
svlachavas • 770
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324
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Answer: A: How to perform a differential expression analysis from TCGA file EBPlusPlusAdjus
15 months ago
svlachavas • 770
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354
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Answer: A: RNASeq DE analysis starts from different DESeq2 normalized data, TMM normalized
15 months ago
svlachavas • 770
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226
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Answer: A: Finding gene targets for a list of transcription factors
16 months ago
svlachavas • 770
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291
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Comment: C: Perform correlation analysis between miRNA and mRNA gene expression data on the
21 months ago
svlachavas • 770
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1
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291
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Comment: C: Perform correlation analysis between miRNA and mRNA gene expression data on the
21 months ago
svlachavas • 770
4
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4
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291
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Perform correlation analysis between miRNA and mRNA gene expression data on the same TCGA dataset based on the curatedTCGAData
curatedTCGAData MultiAssayExperiment multiomics TCGA
21 months ago
svlachavas • 770 • updated 21 months ago
Levi Waldron 1.1k
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171
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Paired DE analysis in edgeR with trios of samples while blocking for various confounders
edger rnaseq paired analysis design matrix
21 months ago
svlachavas • 770
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1
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252
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Comment: C: Correct annotation R package for human clariom array analysis
22 months ago
svlachavas • 770
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1
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252
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Comment: C: Correct annotation R package for human clariom array analysis
22 months ago
svlachavas • 770
1
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5
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252
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Correct annotation R package for human clariom array analysis
clariom oligo affycoretools pd.hugene.2.0.st
22 months ago
svlachavas • 770 • updated 22 months ago
James W. MacDonald 55k
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486
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Comment: C: Taking into account strong batch effect in microarray differential expression an
24 months ago
svlachavas • 770
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1
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486
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Comment: C: Taking into account strong batch effect in microarray differential expression an
24 months ago
svlachavas • 770
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2
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486
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Comment: C: Taking into account strong batch effect in microarray differential expression an
24 months ago
svlachavas • 770
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13
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486
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Taking into account strong batch effect in microarray differential expression analysis with limma
limma microarray hugeneST batch effect DE
24 months ago
svlachavas • 770 • updated 24 months ago
Ryan C. Thompson 7.6k
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1
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486
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Comment: C: Taking into account strong batch effect in microarray differential expression an
24 months ago
svlachavas • 770
3
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3
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378
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Apply different cutoffs with edgeR pipeline and glmTreat for RNA-Seq DEG analysis
edger differential gene expression glmtreat
2.2 years ago
svlachavas • 770 • updated 2.2 years ago
Gordon Smyth 41k
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496
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Comment: C: Explanation of mroast results for specific biological processes and error with b
2.3 years ago
svlachavas • 770
520 results • Page 1 of 11
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