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251
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Combine MAF, GISTIC, and clinical data using maftools
mutation TCGAbiolinks maftools TCGA
4 months ago by melissachua90 ▴ 70
0
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3
replies
479
views
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
1
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4
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1.0k
views
Retrieving single-cell dataset from GEO database
seurat GEO r single-cell
updated 8 months ago by 43k • written 8 months ago by ▴ 70
0
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2
replies
675
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Limma differential expression analysis across subtypes
differential-expression limma
10 months ago by melissachua90 ▴ 70
4
votes
21
replies
2.7k
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Limma returned only positive logFC values
edgeR differential-expression deg limma
10 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
0
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0
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322
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Correlation matrix for mutation vs other omics types
TCGA multi-omics mutation omics maftools
15 months ago by melissachua90 ▴ 70
0
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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
replies
736
views
How to replace Gene Symbols with Ensembl ID?
r biomart
updated 18 months ago by ▴ 310 • written 18 months ago by ▴ 70
0
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0
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385
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GSEApy
gsea gseapy
18 months ago by melissachua90 ▴ 70
1
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3
replies
632
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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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0
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352
views
GDCprepare truncated when downloading TCGA methylation data
GDCquery GDCprepare R TCGA
19 months ago by melissachua90 ▴ 70
0
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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
reply
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
1
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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
0
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2
replies
849
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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
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
0
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0
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408
views
PyGNA
PyGNA network analysis geneset
20 months ago by melissachua90 ▴ 70
0
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2
replies
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
replies
388
views
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
0
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0
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365
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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
0
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0
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645
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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
0
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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
0
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0
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380
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How to find clinical information from cBioPortal?
cbioportal TCGA
24 months ago by melissachua90 ▴ 70
1
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7
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2.0k
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If R package is already install - load it; if not installed, install it
R
updated 24 months ago by 43k • written 2.0 years ago by ▴ 70
0
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7
replies
1.4k
views
Filter out low coverage contigs
bash contigs
updated 24 months ago by 21k • written 2.0 years ago by ▴ 70
2
votes
1
reply
1.3k
views
Samtools coverage vs samtools depth for % coverage
samtools
updated 2.0 years ago by 100k • written 2.0 years ago by ▴ 70
0
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4
replies
2.3k
views
Estimate K-mer size for de novo assembly
de novo assembly soapdenovo estimation kmergenie K-mer
updated 2.0 years ago by ★ 27k • written 2.0 years ago by ▴ 70
3
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5
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1.2k
views
[E::bwa_idx_load_from_disk] fail to locate the index files
alignment BWA
2.0 years ago by melissachua90 ▴ 70
8
votes
3
replies
824
views
MultiQC output shows that data processing steps are ineffective
FastQC trimming
updated 11 months ago by 43k • written 2.0 years ago by ▴ 70
1
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1
reply
2.2k
views
How do I combine MAF files with clinical data to perform clinical enrichment analysis?
maftools maf mutation
updated 10 months ago by 43k • written 2.1 years ago by ▴ 70
5
votes
2
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894
views
How to determine the K-mer size?
k-mer
updated 2.0 years ago by ★ 27k • written 2.0 years ago by ▴ 70
0
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5
replies
850
views
Reference-based alignment using MUSKET
parallel HPC reference-based alignment MUSKET
updated 2.0 years ago by ★ 27k • written 2.0 years ago by ▴ 70
1
vote
2
replies
965
views
BBDuk returned java.lang.AssertionError
fasta bbduk fastq ngs
updated 2.0 years ago by 142k • written 2.0 years ago by ▴ 70
0
votes
1
reply
493
views
Paired-end dataset from SRA database
paired-end sra
updated 2.0 years ago by 82k • written 2.0 years ago by ▴ 70
0
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4
replies
667
views
Efficient way to download SRA dataset
sra
updated 2.0 years ago by 4.6k • written 2.0 years ago by ▴ 70
1
vote
3
replies
728
views
Fastq-dump warning: too many reads at spot id
fastq-dump
updated 2.0 years ago by ★ 2.1k • written 2.0 years ago by ▴ 70
0
votes
2
replies
665
views
Pathway databases for machine learning
pathway machine database CNN learning
updated 2.0 years ago by 43k • written 2.0 years ago by ▴ 70
0
votes
4
replies
751
views
Missing SAM header when piping the samtools mpileup output to a VarScan call
samtools varscan
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 70
0
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4
replies
949
views
Varscan output variant file - is it the "true" file?
varscan
updated 2.1 years ago by 82k • written 2.1 years ago by ▴ 70
1
vote
1
reply
1.0k
views
IGV "Cannot find feature or locus" error
IGV
updated 2.1 years ago by 3.2k • written 2.1 years ago by ▴ 70
0
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5
replies
1.0k
views
How do I load bam file and idx.fa file to the IGV browser?
igv
updated 2.1 years ago by 142k • written 2.1 years ago by ▴ 70
1
vote
5
replies
1.1k
views
Use RSEM and Bowtie2 to align paired-end sequences
bowtie2 rsem
updated 2.1 years ago by 82k • written 2.1 years ago by ▴ 70
1
vote
2
replies
854
views
Bowtie produced empty .sam file
bowtie
updated 2.1 years ago by 11k • written 2.1 years ago by ▴ 70
0
votes
3
replies
710
views
Bowtie: Find the tradeoffs between seed length argument
bowtie
updated 2.1 years ago by 82k • written 2.1 years ago by ▴ 70
0
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15
replies
2.2k
views
Bowtie: How do I map files to reference genome?
bowtie
updated 2.1 years ago by 8.7k • written 2.1 years ago by ▴ 70
0
votes
5
replies
979
views
How do I install MAQ software on Ubuntu?
MAQ
updated 2.1 years ago by ★ 2.9k • written 2.1 years ago by ▴ 70
0
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5
replies
822
views
How to generate paired-end FASTQ files from a reference sequence?
MAQ
updated 2.1 years ago by 142k • written 2.1 years ago by ▴ 70
0
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0
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331
views
How do I add annotation information to ped file and run on PLINK?
plink r bed snps dplyr
2.1 years ago by melissachua90 ▴ 70
71 results • Page 1 of 2
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