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0
votes
2
replies
746
views
How to generate table_annovar from VCF input?
vcf annovar
updated 13 months ago by 166k • written 13 months ago by ▴ 70
2
votes
1
reply
645
views
Failed to open VCF file
GATK sentieon BWA-MEM
updated 14 months ago by 166k • written 14 months ago by ▴ 70
0
votes
0
replies
519
views
Combine MAF, GISTIC, and clinical data using maftools
mutation TCGAbiolinks maftools TCGA
19 months ago by melissachua90 ▴ 70
0
votes
3
replies
886
views
Appropriate genome reference for converting TCGA VCF files to MAF
maf vcf vcf2maf TCGA
updated 19 months ago by ★ 1.3k • written 20 months ago by ▴ 70
1
vote
4
replies
2.1k
views
Retrieving single-cell dataset from GEO database
seurat GEO r single-cell
updated 22 months ago by 45k • written 23 months ago by ▴ 70
0
votes
2
replies
1.0k
views
Limma differential expression analysis across subtypes
differential-expression limma
2.0 years ago by melissachua90 ▴ 70
4
votes
21
replies
4.4k
views
Limma returned only positive logFC values
edgeR differential-expression deg limma
2.0 years ago by melissachua90 ▴ 70
0
votes
1
reply
743
views
How to determine the optimal number of clusters?
clustering clusters
updated 2.4 years ago by 11k • written 2.4 years ago by ▴ 70
0
votes
0
replies
528
views
Correlation matrix for mutation vs other omics types
TCGA multi-omics mutation omics maftools
2.5 years ago by melissachua90 ▴ 70
0
votes
0
replies
524
views
How to find TCGA samples with multiple chromosomal gains?
mutation tcga maftools
2.5 years ago by melissachua90 ▴ 70
1
vote
2
replies
1.1k
views
How to replace Gene Symbols with Ensembl ID?
r biomart
updated 2.7 years ago by ▴ 420 • written 2.7 years ago by ▴ 70
0
votes
0
replies
789
views
GSEApy
gsea gseapy
2.7 years ago by melissachua90 ▴ 70
1
vote
3
replies
953
views
"EpiMutation"
mutation TCGA epigenetics
updated 2.7 years ago by 5.0k • written 2.7 years ago by ▴ 70
0
votes
0
replies
520
views
GDCprepare truncated when downloading TCGA methylation data
GDCquery GDCprepare R TCGA
2.7 years ago by melissachua90 ▴ 70
0
votes
0
replies
611
views
Unable to run cisTarget (pySCENIC)
pySCENIC
2.8 years ago by melissachua90 ▴ 70
1
vote
1
reply
1.7k
views
Create the design matrix for limma differential expression analysis.
gene differential expression dge limma
updated 2.8 years ago by ★ 8.2k • written 2.8 years ago by ▴ 70
1
vote
0
replies
805
views
Visualization of networks inferred using GrnBoost2 on bulk mRNA expression data
python inference network visualization GrnBoost2
2.8 years ago by melissachua90 ▴ 70
0
votes
2
replies
1.3k
views
Retrieve transcription factors from gene set using biomaRt
factors R transcription biomaRt
updated 2.9 years ago by ▴ 60 • written 2.9 years ago by ▴ 70
0
votes
13
replies
13k
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 2.9 years ago by 5.0k • written 2.9 years ago by ▴ 70
0
votes
0
replies
663
views
PyGNA
PyGNA network analysis geneset
2.9 years ago by melissachua90 ▴ 70
0
votes
2
replies
1.3k
views
How to normalize microarray data using Python?
normalization Affymetrix microarray
3.0 years ago by melissachua90 ▴ 70
0
votes
0
replies
602
views
What type of plots is suitable for time-dependent treatment on gene expression for each patient?
time-series plot visualization plotly
3.0 years ago by melissachua90 ▴ 70
0
votes
0
replies
554
views
How to subset specific genes from microarray dataset using Python?
time-series affymetrix pandas microarray
3.0 years ago by melissachua90 ▴ 70
0
votes
0
replies
918
views
CNV annotation using GAIA
cnv gaia
3.0 years ago by melissachua90 ▴ 70
0
votes
0
replies
601
views
scRNA-seq filtering thresholds
filtering scRNA-seq
3.1 years ago by melissachua90 ▴ 70
0
votes
2
replies
1.4k
views
Interpret stacked violin plots
visualization sequencing plot violin single-cell data
updated 3.1 years ago by ★ 1.9k • written 3.1 years ago by ▴ 70
0
votes
0
replies
576
views
How to find clinical information from cBioPortal?
cbioportal TCGA
3.2 years ago by melissachua90 ▴ 70
1
vote
7
replies
3.6k
views
If R package is already install - load it; if not installed, install it
R
updated 3.2 years ago by 45k • written 3.2 years ago by ▴ 70
0
votes
7
replies
2.0k
views
Filter out low coverage contigs
bash contigs
updated 3.2 years ago by 22k • written 3.2 years ago by ▴ 70
2
votes
1
reply
2.8k
views
Samtools coverage vs samtools depth for % coverage
samtools
updated 3.2 years ago by 102k • written 3.2 years ago by ▴ 70
0
votes
4
replies
4.0k
views
Estimate K-mer size for de novo assembly
de novo assembly soapdenovo estimation kmergenie K-mer
updated 3.2 years ago by ★ 29k • written 3.2 years ago by ▴ 70
3
votes
5
replies
1.8k
views
[E::bwa_idx_load_from_disk] fail to locate the index files
alignment BWA
3.2 years ago by melissachua90 ▴ 70
8
votes
3
replies
1.2k
views
MultiQC output shows that data processing steps are ineffective
FastQC trimming
updated 2.2 years ago by 45k • written 3.2 years ago by ▴ 70
1
vote
1
reply
3.1k
views
How do I combine MAF files with clinical data to perform clinical enrichment analysis?
maftools maf mutation
updated 2.1 years ago by 45k • written 3.3 years ago by ▴ 70
6
votes
2
replies
1.7k
views
How to determine the K-mer size?
k-mer
updated 3.2 years ago by ★ 29k • written 3.2 years ago by ▴ 70
0
votes
5
replies
1.3k
views
Reference-based alignment using MUSKET
parallel HPC reference-based alignment MUSKET
updated 3.2 years ago by ★ 29k • written 3.2 years ago by ▴ 70
1
vote
2
replies
1.3k
views
BBDuk returned java.lang.AssertionError
fasta bbduk fastq ngs
updated 3.2 years ago by 152k • written 3.2 years ago by ▴ 70
0
votes
1
reply
726
views
Paired-end dataset from SRA database
paired-end sra
updated 3.2 years ago by 88k • written 3.2 years ago by ▴ 70
0
votes
4
replies
960
views
Efficient way to download SRA dataset
sra
updated 3.2 years ago by 5.1k • written 3.2 years ago by ▴ 70
1
vote
3
replies
1.1k
views
Fastq-dump warning: too many reads at spot id
fastq-dump
updated 3.2 years ago by ★ 2.1k • written 3.2 years ago by ▴ 70
0
votes
2
replies
950
views
Pathway databases for machine learning
pathway machine database CNN learning
updated 3.2 years ago by 45k • written 3.2 years ago by ▴ 70
0
votes
4
replies
1.0k
views
Missing SAM header when piping the samtools mpileup output to a VarScan call
samtools varscan
updated 3.2 years ago by 45k • written 3.2 years ago by ▴ 70
0
votes
4
replies
1.4k
views
Varscan output variant file - is it the "true" file?
varscan
updated 3.2 years ago by 88k • written 3.2 years ago by ▴ 70
1
vote
1
reply
1.5k
views
IGV "Cannot find feature or locus" error
IGV
updated 3.2 years ago by 3.3k • written 3.2 years ago by ▴ 70
0
votes
5
replies
1.4k
views
How do I load bam file and idx.fa file to the IGV browser?
igv
updated 3.2 years ago by 152k • written 3.2 years ago by ▴ 70
1
vote
5
replies
1.6k
views
Use RSEM and Bowtie2 to align paired-end sequences
bowtie2 rsem
updated 3.2 years ago by 88k • written 3.2 years ago by ▴ 70
1
vote
2
replies
1.3k
views
Bowtie produced empty .sam file
bowtie
updated 3.3 years ago by 11k • written 3.3 years ago by ▴ 70
0
votes
3
replies
1.0k
views
Bowtie: Find the tradeoffs between seed length argument
bowtie
updated 3.3 years ago by 88k • written 3.3 years ago by ▴ 70
0
votes
15
replies
3.7k
views
Bowtie: How do I map files to reference genome?
bowtie
updated 3.3 years ago by 9.0k • written 3.3 years ago by ▴ 70
0
votes
5
replies
1.5k
views
How do I install MAQ software on Ubuntu?
MAQ
updated 3.3 years ago by ★ 2.9k • written 3.3 years ago by ▴ 70
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