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Combine MAF, GISTIC, and clinical data using maftools
mutation TCGAbiolinks maftools TCGA
4 months ago by melissachua90 ▴ 70
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480
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Comment: Comment: Appropriate genome reference for converting TCGA VCF files to MAF
5 months ago by melissachua90 ▴ 70
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3
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480
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Appropriate genome reference for converting TCGA VCF files to MAF
maf vcf vcf2maf TCGA
updated 5 months ago by ★ 1.2k • written 5 months ago by ▴ 70
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1.0k
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Comment: Comment: Retrieving single-cell dataset from GEO database
8 months ago by melissachua90 ▴ 70
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4
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1.0k
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Retrieving single-cell dataset from GEO database
seurat GEO r single-cell
updated 8 months ago by 43k • written 8 months ago by ▴ 70
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676
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Comment: Comment: Limma differential expression analysis across subtypes
10 months ago by melissachua90 ▴ 70
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2
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676
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Limma differential expression analysis across subtypes
differential-expression limma
10 months ago by melissachua90 ▴ 70
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2.7k
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Comment: Comment: Limma returned only positive logFC values
10 months ago by melissachua90 ▴ 70
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0
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2.7k
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Comment: Comment: Limma returned only positive logFC values
10 months ago by melissachua90 ▴ 70
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0
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2.7k
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Comment: Comment: Limma returned only positive logFC values
10 months ago by melissachua90 ▴ 70
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1
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2.7k
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Comment: Comment: Limma returned only positive logFC values
10 months ago by melissachua90 ▴ 70
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2
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2.7k
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Comment: Comment: Limma returned only positive logFC values
10 months ago by melissachua90 ▴ 70
0
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1
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2.7k
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Comment: Comment: Limma returned only positive logFC values
11 months ago by melissachua90 ▴ 70
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1
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2.7k
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Comment: Comment: Limma returned only positive logFC values
11 months ago by melissachua90 ▴ 70
4
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21
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2.7k
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Limma returned only positive logFC values
edgeR differential-expression deg limma
10 months ago by melissachua90 ▴ 70
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0
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2.7k
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Comment: Comment: Limma returned only positive logFC values
11 months ago by melissachua90 ▴ 70
0
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1
reply
2.7k
views
Comment: Comment: Limma returned only positive logFC values
11 months ago by melissachua90 ▴ 70
0
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0
replies
2.7k
views
Comment: Comment: Limma returned only positive logFC values
11 months ago by melissachua90 ▴ 70
0
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1
reply
2.7k
views
Comment: Comment: Limma returned only positive logFC values
11 months ago by melissachua90 ▴ 70
0
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1
reply
454
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How to determine the optimal number of clusters?
clustering clusters
updated 14 months ago by 11k • written 14 months ago by ▴ 70
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323
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Correlation matrix for mutation vs other omics types
TCGA multi-omics mutation omics maftools
15 months ago by melissachua90 ▴ 70
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0
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331
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How to find TCGA samples with multiple chromosomal gains?
mutation tcga maftools
16 months ago by melissachua90 ▴ 70
1
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2
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737
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How to replace Gene Symbols with Ensembl ID?
r biomart
updated 18 months ago by ▴ 310 • written 18 months ago by ▴ 70
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386
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GSEApy
gsea gseapy
18 months ago by melissachua90 ▴ 70
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1
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633
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Comment: Comment: "EpiMutation"
18 months ago by melissachua90 ▴ 70
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3
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633
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"EpiMutation"
mutation TCGA epigenetics
updated 18 months ago by 3.9k • written 18 months ago by ▴ 70
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352
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GDCprepare truncated when downloading TCGA methylation data
GDCquery GDCprepare R TCGA
19 months ago by melissachua90 ▴ 70
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0
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414
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Unable to run cisTarget (pySCENIC)
pySCENIC
19 months ago by melissachua90 ▴ 70
1
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1
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1.0k
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Create the design matrix for limma differential expression analysis.
gene differential expression dge limma
updated 19 months ago by ★ 7.1k • written 19 months ago by ▴ 70
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0
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480
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Visualization of networks inferred using GrnBoost2 on bulk mRNA expression data
python inference network visualization GrnBoost2
19 months ago by melissachua90 ▴ 70
4
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4
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1.4k
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Forum: Bioinformatics analogies
Bioinformatics
updated 20 months ago by 100k • written 20 months ago by ▴ 70
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2
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852
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Retrieve transcription factors from gene set using biomaRt
factors R transcription biomaRt
updated 20 months ago by ▴ 60 • written 20 months ago by ▴ 70
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1
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8.5k
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Comment: Comment: How to deal with `'select()' returned 1:many mapping between keys and columns` w
20 months ago by melissachua90 ▴ 70
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0
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8.5k
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Comment: Comment: How to retrieve Entrez IDs using Gene Symbols in R?
20 months ago by melissachua90 ▴ 70
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1
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8.5k
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Comment: Comment: How to retrieve Entrez IDs using Gene Symbols in R?
20 months ago by melissachua90 ▴ 70
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1
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8.5k
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Comment: Comment: How to retrieve Entrez IDs using Gene Symbols in R?
20 months ago by melissachua90 ▴ 70
0
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1
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8.5k
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Comment: Comment: How to retrieve Entrez IDs using Gene Symbols in R?
20 months ago by melissachua90 ▴ 70
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1
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8.5k
views
Comment: Comment: How to retrieve Entrez IDs using Gene Symbols in R?
20 months ago by melissachua90 ▴ 70
0
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13
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8.5k
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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 20 months ago by 3.9k • written 20 months ago by ▴ 70
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0
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408
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PyGNA
PyGNA network analysis geneset
20 months ago by melissachua90 ▴ 70
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0
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921
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Comment: Comment: How to normalize microarray data using Python?
21 months ago by melissachua90 ▴ 70
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2
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921
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How to normalize microarray data using Python?
normalization Affymetrix microarray
21 months ago by melissachua90 ▴ 70
0
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0
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389
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What type of plots is suitable for time-dependent treatment on gene expression for each patient?
time-series plot visualization plotly
21 months ago by melissachua90 ▴ 70
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0
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366
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How to subset specific genes from microarray dataset using Python?
time-series affymetrix pandas microarray
21 months ago by melissachua90 ▴ 70
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0
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646
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CNV annotation using GAIA
cnv gaia
22 months ago by melissachua90 ▴ 70
0
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0
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377
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scRNA-seq filtering thresholds
filtering scRNA-seq
23 months ago by melissachua90 ▴ 70
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2
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1.1k
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Interpret stacked violin plots
visualization sequencing plot violin single-cell data
updated 23 months ago by ★ 1.8k • written 23 months ago by ▴ 70
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0
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381
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How to find clinical information from cBioPortal?
cbioportal TCGA
24 months ago by melissachua90 ▴ 70
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1
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2.0k
views
Comment: Comment: If R package is already install - load it; if not installed, install it
2.0 years ago by melissachua90 ▴ 70
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1
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2.0k
views
Comment: Comment: If R package is already install - load it; if not installed, install it
2.0 years ago by melissachua90 ▴ 70
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