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1
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4
replies
1.7k
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ConsensusClusterPlus: How to extract most contributing features for each cluster
R consensusclusterplus
updated 7 months ago by 3.9k • written 3.2 years ago by ★ 4.1k
26
votes
35
replies
32k
views
16 follow
Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
mpileup
updated 15 months ago by ▴ 10 • written 10.1 years ago by ★ 4.1k
4
votes
7
replies
2.2k
views
TCGA library type information
tcga
updated 19 months ago by ★ 1.2k • written 3.0 years ago by ★ 4.1k
3
votes
3
replies
4.2k
views
using hclust object from FactoMineR::HCPC to force clustering in pheatmap
RNA-Seq factorminer PCA HCPC
3.8 years ago by komal.rathi ★ 4.1k
43
votes
12
replies
39k
views
9 follow
Bedtools Genomecoveragebed Usage : How To Create A Genome File?
bedtools
updated 2.5 years ago by 43k • written 11.0 years ago by ★ 4.1k
4
votes
9
replies
9.7k
views
Download all eQTL data for all the 9 tissues from GTEx Portal
GTEx-Portal eQTL
updated 2.3 years ago by 43k • written 9.9 years ago by ★ 4.1k
6
votes
3
replies
4.5k
views
How to get known canonical transcript information from UCSC for a specific gencode version
gencode ucsc canonical transcripts
5.0 years ago by komal.rathi ★ 4.1k
6
votes
4
replies
5.9k
views
GATK ASEReadCounter: Downstream analysis for identifying allele specific expression
RNA-Seq allele-specific expression
updated 5.3 years ago by 6.6k • written 6.8 years ago by ★ 4.1k
0
votes
3
replies
1.6k
views
How to determine RNA-seq samples from dbGaP metadata
dbgap metadata
updated 5.7 years ago by 5.7k • written 5.7 years ago by ★ 4.1k
6
votes
6
replies
4.2k
views
Rnaseq Library Quantification
rnaseq library
updated 6.2 years ago by 35k • written 10.6 years ago by ★ 4.1k
22
votes
8
replies
27k
views
R DESeq: What exactly is Variance Stabilizating Transformation?
R DESeq VST
updated 2.4 years ago by 43k • written 9.7 years ago by ★ 4.1k
8
votes
2
replies
2.5k
views
Why does GFF prepared using dexseq_prepare_annotation shows different exon number than UCSC genome browser
dexseq_prepare_annotation dexseq exons
updated 6.6 years ago by 104k • written 6.6 years ago by ★ 4.1k
1
vote
2
replies
2.2k
views
Filter bam files using a bed file: Why is the mate missing?
RNA-Seq Samtools
6.6 years ago by komal.rathi ★ 4.1k
2
votes
5
replies
4.3k
views
exon level quantification using htseq count
htseq-count RNA-Seq exon quantifications
updated 6.6 years ago by 104k • written 6.6 years ago by ★ 4.1k
0
votes
3
replies
4.2k
views
RSEM output interpretation
rsem
6.7 years ago by komal.rathi ★ 4.1k
0
votes
6
replies
3.1k
views
IGV color interpretation by insert size
igv
updated 6.8 years ago by 100k • written 6.8 years ago by ★ 4.1k
0
votes
6
replies
2.0k
views
Is it possible/recommended to trim RNA-Seq reads to a specific length
trim RNA-Seq chimeraScan STAR-Fusion
updated 7.0 years ago by 20 • written 7.2 years ago by ★ 4.1k
1
vote
3
replies
3.3k
views
How to create an AffyBatch object using a data matrix?
affy affyBatch matrix
7.1 years ago by komal.rathi ★ 4.1k
4
votes
2
replies
1.9k
views
RNASeq differential expression: How to deal with few genes with extremely high expression levels
RNA-Seq mtDNA limma voom
updated 7.1 years ago by 8.7k • written 7.1 years ago by ★ 4.1k
1
vote
2
replies
1.6k
views
TCGA disease subtype information
tcga
updated 7.3 years ago by 7.5k • written 7.3 years ago by ★ 4.1k
5
votes
8
replies
2.9k
views
Visualizing hg19 and hg38 FPKMs in a single plot
RNA-Seq
updated 7.5 years ago by 11k • written 7.5 years ago by ★ 4.1k
3
votes
2
replies
2.1k
views
TARGET Pediatric Cancer Code Table
TARGET Code
7.5 years ago by komal.rathi ★ 4.1k
0
votes
0
replies
2.5k
views
CRLMM: Which array type work with which annotation package
crlmm
7.6 years ago by komal.rathi ★ 4.1k
4
votes
5
replies
2.6k
views
Convert specific regions in bam file to vcf and annotating the vcf
exome sequencing bam vcf subset
7.7 years ago by komal.rathi ★ 4.1k
30
votes
23
replies
32k
views
10 follow
TCGA: Does TCGA cancer studies have mRNA expression data for Control/Normal samples?
RSEM controls TCGA normals RNASeq
updated 3.0 years ago by 43k • written 9.8 years ago by ★ 4.1k
1
vote
2
replies
2.2k
views
Some Ways To Analyze Picard Estimatelibrarycomplexity Results
picard
updated 7.8 years ago by 20 • written 10.6 years ago by ★ 4.1k
5
votes
2
replies
2.8k
views
Batch query obsolete gene names to get current HGNC symbol
gene symbols obsolete biomart genecards
7.9 years ago by komal.rathi ★ 4.1k
5
votes
6
replies
3.4k
views
Can't access DAVID
DAVID
updated 16 months ago by 43k • written 8.9 years ago by ★ 4.1k
0
votes
6
replies
2.2k
views
Identify genes with extracellular matrix domains
protein domain compartments extracellular matrix
updated 7.9 years ago by 18k • written 7.9 years ago by ★ 4.1k
30
votes
8
replies
56k
views
7 follow
R: How to convert log2FC (Fold Change) obtained by limma's topTable() function to FC
limma microarray topTable R
updated 22 months ago by 43k • written 10.0 years ago by ★ 4.1k
1
vote
3
replies
4.2k
views
How to sort fastq.gz files efficiently
fastq sort
updated 13 months ago by 43k • written 8.2 years ago by ★ 4.1k
5
votes
3
replies
6.7k
views
HISAT (Transcript Alignment) and StringTie (Transcript Assembly)
RNA-Seq HISAT StringTie
updated 22 months ago by 43k • written 9.6 years ago by ★ 4.1k
6
votes
8
replies
6.3k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
voom RNA-Seq spike-in deseq limma
updated 21 months ago by 43k • written 8.5 years ago by ★ 4.1k
3
votes
3
replies
9.4k
views
How to add tss_id and p_id in an Ensembl GTF (or any GTF other than that generated by cufflinks)
cuffcompare
updated 2.4 years ago by 43k • written 9.7 years ago by ★ 4.1k
2
votes
8
replies
4.0k
views
Cuffquant Error:- BAM error: CIGAR op has zero length
mm10 bam ensembl75 gsnap cuffquant
updated 2.3 years ago by 43k • written 9.6 years ago by ★ 4.1k
0
votes
0
replies
3.6k
views
How to find Significant Trans- Interactions in HiC data
GOTHiC HiCUP HiC Bowtie2
updated 22 months ago by 43k • written 9.1 years ago by ★ 4.1k
23
votes
16
replies
13k
views
How to remove reads with hard/soft clipping along with its mate?
gsnap rna-seq
updated 22 months ago by 43k • written 9.1 years ago by ★ 4.1k
2
votes
6
replies
5.1k
views
KEGG Pathway elements' text color code
kegg-pathway
updated 2.0 years ago by 43k • written 9.2 years ago by ★ 4.1k
4
votes
3
replies
6.4k
views
Download ChromHMM tracks H3K27ac marks (as BED file) from Roadmap
BED UCSC-Genome-Browser H3k27ac Roadmap ChromHMM
updated 2.3 years ago by 43k • written 9.6 years ago by ★ 4.1k
3
votes
3
replies
3.1k
views
Detection of genes expressed above background for Gene ST Arrays (as opposed to Exon ST Arrays)
GeneST genechip background expression
updated 2.3 years ago by 43k • written 9.8 years ago by ★ 4.1k
2
votes
3
replies
4.6k
views
Error in htseq-count: "Malformed SAM line: MRNM == '*' although flag bit &0x0008 cleared"
htseq-count
updated 2.9 years ago by 43k • written 9.7 years ago by ★ 4.1k
36
votes
4
replies
51k
views
TCGA: What are mRNA expression z-scores? Does TCGA have mRNA expression from controls?
z-scores TCGA RSEM
updated 3.0 years ago by 43k • written 9.8 years ago by ★ 4.1k
8
votes
4
replies
4.2k
views
Normalization of RNASeq read counts without conditions
readcounts RNA-Seq limma vst deseq
updated 2.5 years ago by 43k • written 9.8 years ago by ★ 4.1k
5
votes
1
reply
5.6k
views
Interpreting Estimate Library Complexity Output
Picard EstimateLibraryComplexity
updated 2.5 years ago by 43k • written 9.9 years ago by ★ 4.1k
9
votes
6
replies
6.6k
views
FastQC and EstimateLibrarySize (Picard): Library Complexity and/or Duplicated Reads
EstimateLibrarySize FastQC PicardTools
updated 2.5 years ago by 43k • written 9.9 years ago by ★ 4.1k
1
vote
6
replies
4.6k
views
Warning in CuffDiff when using novel transcripts from CuffMerge as input
cuffdiff novel-transcripts
updated 2.2 years ago by 43k • written 9.9 years ago by ★ 4.1k
4
votes
2
replies
7.4k
views
How does DESeq2 handle the read-counts assigned to special counters in HTSeq-count output?
htseq-count RNA-Seq DESeq2
updated 2.6 years ago by 43k • written 10.1 years ago by ★ 4.1k
1
vote
1
reply
4.0k
views
RNASeq: Normalization and Differential Gene Expression on lncRNAs and Protein-coding genes
RNA-Seq vst normalization limma
updated 2.6 years ago by 43k • written 10.1 years ago by ★ 4.1k
2
votes
5
replies
5.7k
views
R Deseq2 Error: Inv(): Matrix Appears To Be Singular
r
10.1 years ago by komal.rathi ★ 4.1k
0
votes
0
replies
3.2k
views
No Coverage Information In *.Fpkm_Tracking Files Obtained From Cuffdiff Output
cuffdiff fpkm coverage
updated 10.1 years ago by 20 • written 10.4 years ago by ★ 4.1k
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