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967
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How to generate table_annovar from VCF input?
vcf annovar
updated 18 months ago by 166k • written 18 months ago by ▴ 70
2
votes
1
reply
790
views
Failed to open VCF file
GATK sentieon BWA-MEM
updated 18 months ago by 166k • written 18 months ago by ▴ 70
0
votes
0
replies
666
views
Combine MAF, GISTIC, and clinical data using maftools
mutation TCGAbiolinks maftools TCGA
23 months ago by melissachua90 ▴ 70
0
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1
reply
1.1k
views
Comment: Comment: Appropriate genome reference for converting TCGA VCF files to MAF
2.0 years ago by melissachua90 ▴ 70
0
votes
3
replies
1.1k
views
Appropriate genome reference for converting TCGA VCF files to MAF
maf vcf vcf2maf TCGA
updated 2.0 years ago by ★ 1.3k • written 2.0 years ago by ▴ 70
0
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1
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2.8k
views
Comment: Comment: Retrieving single-cell dataset from GEO database
2.3 years ago by melissachua90 ▴ 70
1
vote
4
replies
2.8k
views
Retrieving single-cell dataset from GEO database
seurat GEO r single-cell
updated 2.3 years ago by 45k • written 2.3 years ago by ▴ 70
0
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0
replies
1.2k
views
Comment: Comment: Limma differential expression analysis across subtypes
2.4 years ago by melissachua90 ▴ 70
0
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2
replies
1.2k
views
Limma differential expression analysis across subtypes
differential-expression limma
2.4 years ago by melissachua90 ▴ 70
0
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0
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5.2k
views
Comment: Comment: Limma returned only positive logFC values
2.4 years ago by melissachua90 ▴ 70
0
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0
replies
5.2k
views
Comment: Comment: Limma returned only positive logFC values
2.5 years ago by melissachua90 ▴ 70
0
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0
replies
5.2k
views
Comment: Comment: Limma returned only positive logFC values
2.5 years ago by melissachua90 ▴ 70
0
votes
1
reply
5.2k
views
Comment: Comment: Limma returned only positive logFC values
2.5 years ago by melissachua90 ▴ 70
0
votes
2
replies
5.2k
views
Comment: Comment: Limma returned only positive logFC values
2.5 years ago by melissachua90 ▴ 70
0
votes
1
reply
5.2k
views
Comment: Comment: Limma returned only positive logFC values
2.5 years ago by melissachua90 ▴ 70
0
votes
1
reply
5.2k
views
Comment: Comment: Limma returned only positive logFC values
2.5 years ago by melissachua90 ▴ 70
4
votes
21
replies
5.2k
views
Limma returned only positive logFC values
edgeR differential-expression deg limma
2.4 years ago by melissachua90 ▴ 70
0
votes
0
replies
5.2k
views
Comment: Comment: Limma returned only positive logFC values
2.5 years ago by melissachua90 ▴ 70
0
votes
1
reply
5.2k
views
Comment: Comment: Limma returned only positive logFC values
2.5 years ago by melissachua90 ▴ 70
0
votes
0
replies
5.2k
views
Comment: Comment: Limma returned only positive logFC values
2.5 years ago by melissachua90 ▴ 70
0
votes
1
reply
5.2k
views
Comment: Comment: Limma returned only positive logFC values
2.5 years ago by melissachua90 ▴ 70
0
votes
1
reply
867
views
How to determine the optimal number of clusters?
clustering clusters
updated 2.8 years ago by 11k • written 2.8 years ago by ▴ 70
0
votes
0
replies
643
views
Correlation matrix for mutation vs other omics types
TCGA multi-omics mutation omics maftools
2.9 years ago by melissachua90 ▴ 70
0
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0
replies
619
views
How to find TCGA samples with multiple chromosomal gains?
mutation tcga maftools
2.9 years ago by melissachua90 ▴ 70
1
vote
2
replies
1.3k
views
How to replace Gene Symbols with Ensembl ID?
r biomart
updated 3.1 years ago by ▴ 420 • written 3.1 years ago by ▴ 70
0
votes
0
replies
911
views
GSEApy
gsea gseapy
3.1 years ago by melissachua90 ▴ 70
0
votes
1
reply
1.1k
views
Comment: Comment: "EpiMutation"
3.1 years ago by melissachua90 ▴ 70
1
vote
3
replies
1.1k
views
"EpiMutation"
mutation TCGA epigenetics
updated 3.1 years ago by 5.2k • written 3.1 years ago by ▴ 70
0
votes
0
replies
604
views
GDCprepare truncated when downloading TCGA methylation data
GDCquery GDCprepare R TCGA
3.1 years ago by melissachua90 ▴ 70
0
votes
0
replies
709
views
Unable to run cisTarget (pySCENIC)
pySCENIC
3.1 years ago by melissachua90 ▴ 70
1
vote
1
reply
2.0k
views
Create the design matrix for limma differential expression analysis.
gene differential expression dge limma
updated 3.2 years ago by ★ 8.6k • written 3.2 years ago by ▴ 70
1
vote
0
replies
921
views
Visualization of networks inferred using GrnBoost2 on bulk mRNA expression data
python inference network visualization GrnBoost2
3.2 years ago by melissachua90 ▴ 70
4
votes
4
replies
2.3k
views
Forum: Bioinformatics analogies
Bioinformatics
updated 3.2 years ago by 103k • written 3.2 years ago by ▴ 70
0
votes
2
replies
1.5k
views
Retrieve transcription factors from gene set using biomaRt
factors R transcription biomaRt
updated 3.3 years ago by ▴ 60 • written 3.3 years ago by ▴ 70
0
votes
1
reply
14k
views
Comment: Comment: How to deal with `'select()' returned 1:many mapping between keys and columns` w
3.3 years ago by melissachua90 ▴ 70
0
votes
0
replies
14k
views
Comment: Comment: How to retrieve Entrez IDs using Gene Symbols in R?
3.3 years ago by melissachua90 ▴ 70
0
votes
1
reply
14k
views
Comment: Comment: How to retrieve Entrez IDs using Gene Symbols in R?
3.3 years ago by melissachua90 ▴ 70
0
votes
1
reply
14k
views
Comment: Comment: How to retrieve Entrez IDs using Gene Symbols in R?
3.3 years ago by melissachua90 ▴ 70
0
votes
1
reply
14k
views
Comment: Comment: How to retrieve Entrez IDs using Gene Symbols in R?
3.3 years ago by melissachua90 ▴ 70
0
votes
1
reply
14k
views
Comment: Comment: How to retrieve Entrez IDs using Gene Symbols in R?
3.3 years ago by melissachua90 ▴ 70
0
votes
13
replies
14k
views
How to deal with `'select()' returned 1:many mapping between keys and columns` warning when retrieving Entrez IDs using Gene Symbols in R?
mapids R netgsa entrez
updated 3.3 years ago by 5.2k • written 3.3 years ago by ▴ 70
0
votes
0
replies
748
views
PyGNA
PyGNA network analysis geneset
3.3 years ago by melissachua90 ▴ 70
0
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0
replies
1.5k
views
Comment: Comment: How to normalize microarray data using Python?
3.3 years ago by melissachua90 ▴ 70
0
votes
2
replies
1.5k
views
How to normalize microarray data using Python?
normalization Affymetrix microarray
3.3 years ago by melissachua90 ▴ 70
0
votes
0
replies
701
views
What type of plots is suitable for time-dependent treatment on gene expression for each patient?
time-series plot visualization plotly
3.3 years ago by melissachua90 ▴ 70
0
votes
0
replies
646
views
How to subset specific genes from microarray dataset using Python?
time-series affymetrix pandas microarray
3.3 years ago by melissachua90 ▴ 70
0
votes
0
replies
1.0k
views
CNV annotation using GAIA
cnv gaia
3.4 years ago by melissachua90 ▴ 70
0
votes
0
replies
720
views
scRNA-seq filtering thresholds
filtering scRNA-seq
3.5 years ago by melissachua90 ▴ 70
0
votes
2
replies
1.6k
views
Interpret stacked violin plots
visualization sequencing plot violin single-cell data
updated 3.5 years ago by ★ 1.9k • written 3.5 years ago by ▴ 70
0
votes
0
replies
665
views
How to find clinical information from cBioPortal?
cbioportal TCGA
3.5 years ago by melissachua90 ▴ 70
137 results • Page 1 of 3
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