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CancerData
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Job:
Postdoc for computational biology on cancer omics data analysis at Liang lab of Wistar Institute, Philadelphia, US
omics
cancerdata
Pathways
13 months ago
omicsresearch
• 0
0
votes
2
replies
2.0k
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Error with TCGA package - TCGAbiolinks
TCGAbiolinks
RNASeq
CancerData
updated 2.5 years ago by
Tiago C. Silva
▴ 270 • written 2.6 years ago by
JAcky
• 0
2
votes
3
replies
1.7k
views
Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery
CancerData
limma
RCy3
CancerInSilico
updated 3.2 years ago by
Steve Lianoglou
★ 13k • written 3.3 years ago by
Caitlin
▴ 50
1
vote
1
reply
1.5k
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Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray
GEOquery
cancerdata
MicroarrayData
updated 3.4 years ago by
James W. MacDonald
68k • written 3.4 years ago by
Caitlin
▴ 50
0
votes
0
replies
957
views
Job:
PDRA in Computational Biophysics and Cancer Research, University of Manchester, UK
CancerData
StructuralGenomics
VirusStability
pH-dependence
3.5 years ago
jim.warwicker
• 0
5 results • Page
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Comment: Weird p-values using DESeq2?
by
ATpoint
★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2?
by
Wolfgang Huber
★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Comment: How to visualize these pathways using pathview
by
ingrid.h
• 0
Yes I have seen it, thanks.
Comment: Store Matrix in DataFrame Cell
by
Dario Strbenac
★ 1.6k
It does not appear to work. > DataFrame(name = "test", value = list(matrix(1:4, ncol = 2))) DataFrame with 2 rows and 3 columns …
Comment: Overcoming confounding in batch effect correction
by
Dario Strbenac
★ 1.6k
Actually, it is directly related. ComBat-seq is a part of [sva][1] package. It should use sva tag. [1]: https://bioconductor.org/package…
Votes
A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
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Jim Nemesh
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James W. MacDonald
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16k
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shepherl
4.1k
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