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2
votes
5
replies
2.1k
views
what TCGA biospecimen filter should be selected for retrieving "invasive ductal breast carcinoma" data?
TCGA invasive ductal carcinoma
7.4 years ago by nazaninhoseinkhan ▴ 530
2
votes
5
replies
3.3k
views
Is it correct if we use htseq counts as raw read counts in DESEq2?
RNA-Seq DESeq2 htseqCounts
updated 7.4 years ago by 105k • written 7.4 years ago by ▴ 530
1
vote
3
replies
2.2k
views
HTSeq-counts can not map any reads to gtf file
RNA-Seq htseq-counts no mapped reads
updated 7.4 years ago by 9.0k • written 7.4 years ago by ▴ 530
0
votes
5
replies
16k
views
error in getting results from DESeq2
DESeq2 results error
updated 7.4 years ago by 105k • written 7.4 years ago by ▴ 530
5
votes
3
replies
3.0k
views
Low number of healthy samples in TCGA
TCGA GDC portal Healthy samples or adjacent normal
updated 7.4 years ago by 89k • written 7.4 years ago by ▴ 530
1
vote
1
reply
3.1k
views
removing batch effects from large number of data sets
Microarray batch-effect
updated 19 months ago by 45k • written 7.4 years ago by ▴ 530
0
votes
4
replies
4.7k
views
error in "DESeqDataSetFromMatrix" function in DESeq2
RNA-Seq DESeq2 error message
updated 7.4 years ago by 105k • written 7.4 years ago by ▴ 530
0
votes
0
replies
1.8k
views
Differential co-expression analysis on TCGA transcriptomic data
RNA-Seq miRNA-Seq differential expression
7.5 years ago by nazaninhoseinkhan ▴ 530
1
vote
2
replies
2.3k
views
How to download data for normal solid tissue from GDC using TCG2bed
TCGA2BED Normal data GDC portal
7.5 years ago by nazaninhoseinkhan ▴ 530
0
votes
0
replies
1.5k
views
Drawing heatmap of expression data using GENE-E
Scaling Heatmap GENE-E
7.5 years ago by nazaninhoseinkhan ▴ 530
0
votes
1
reply
2.3k
views
How to change the format of CNV files (.txt) obtained from GDC to accepted formats of Variant Effect Predictor?
CNV GDC
updated 2.3 years ago by 45k • written 7.5 years ago by ▴ 530
0
votes
1
reply
2.4k
views
Removing batch effects between Affymetrix and Agilent platforms using ComBat
Microarray Affymetrix Agilent ComBat
updated 7.5 years ago by 6.7k • written 7.5 years ago by ▴ 530
1
vote
2
replies
6.0k
views
batch effect removal from several RNASeq experiments
RNA-Seq Batch effect removal
7.6 years ago by nazaninhoseinkhan ▴ 530
0
votes
1
reply
1.2k
views
Preparing functional gene set for DECODE program
DECODE Functional gene set
updated 7.6 years ago by 35k • written 7.7 years ago by ▴ 530
3
votes
5
replies
10k
views
Biobase library in R
R
updated 3.6 years ago by 45k • written 10.8 years ago by ▴ 530
0
votes
3
replies
2.1k
views
StringTie error: list index out of range
StringTie error Galaxy
7.8 years ago by nazaninhoseinkhan ▴ 530
0
votes
4
replies
2.6k
views
StringTie cannot be run as a problem in naming convention
StringTie Gene naming convention GTF
updated 7.8 years ago by ★ 1.7k • written 7.8 years ago by ▴ 530
0
votes
1
reply
1.3k
views
cannot permanently delete a collection of data sets to retrieve the memory in GALAXY
collection of data sets permanently delete galaxy
7.8 years ago by nazaninhoseinkhan ▴ 530
1
vote
6
replies
1.9k
views
CuffDiff results does not seem correct
RNA-Seq CuffDiff Galaxy
7.9 years ago by nazaninhoseinkhan ▴ 530
2
votes
1
reply
3.1k
views
Is it correct to consider the genes of grey module resulted from consensus network analysis (WGCNA) as differential expressed?
WGCNA Consensus network Differential expressed
updated 7.9 years ago by 105k • written 7.9 years ago by ▴ 530
3
votes
5
replies
3.1k
views
what to do when adjusted p-values are not acceptable in RNASeq?
RNA-Seq FDR
8.2 years ago by nazaninhoseinkhan ▴ 530
1
vote
9
replies
2.7k
views
Deseq2 does not recognize htseq count outputs
RNA-Seq Deseq2 inputs are not recognized
8.2 years ago by nazaninhoseinkhan ▴ 530
0
votes
7
replies
3.1k
views
problem in loading systemPipeR and RNASeqGene packages in R 3.4.1
r rna-seq genomicRange
updated 8.2 years ago by 45k • written 8.2 years ago by ▴ 530
1
vote
6
replies
4.4k
views
lncRNA target identification
lncRNA Target
updated 8.3 years ago by • 0 • written 9.1 years ago by ▴ 530
2
votes
5
replies
1.6k
views
Ambiguity in Ensembl results for IRGM gene
ensembl transcripts ambiguity
8.3 years ago by nazaninhoseinkhan ▴ 530
0
votes
0
replies
1.4k
views
How many mapped reads is considered as significant in Kraken
next-gen mirobiome mapped reads cutoff
8.5 years ago by nazaninhoseinkhan ▴ 530
1
vote
1
reply
1.4k
views
how to characterize microbes in a fastq file of sewage microbiome
next-gen microbiome analysis
updated 8.5 years ago by 22k • written 8.5 years ago by ▴ 530
0
votes
3
replies
2.3k
views
problem in probeID conversion in Staphylococcus aureus
affyId conversion Staphylococcus aureus gpl1339
updated 8.6 years ago by ▴ 180 • written 8.6 years ago by ▴ 530
16
votes
34
replies
6.8k
views
7 follow
GC percent detection for several number of genes
GC% large number of genes
8.6 years ago by nazaninhoseinkhan ▴ 530
1
vote
4
replies
3.2k
views
error in WGCNA
WGCNA adjacency Error
updated 8.6 years ago by 20 • written 8.7 years ago by ▴ 530
3
votes
1
reply
3.3k
views
WGCNA dealing with missing data
WGCNA missing data cutoff
updated 8.6 years ago by ▴ 840 • written 8.6 years ago by ▴ 530
4
votes
9
replies
2.8k
views
merged paried end RNASeq
rna-seq paired reads merged
8.7 years ago by nazaninhoseinkhan ▴ 530
1
vote
1
reply
4.1k
views
Low-pass whole genome sequencing
next-gen low-pass
updated 8.8 years ago by 9.8k • written 8.8 years ago by ▴ 530
2
votes
2
replies
2.8k
views
Trinity RNASeq DNASeq assembly
next-gen Assembly Trinity
updated 8.8 years ago by ★ 5.2k • written 8.8 years ago by ▴ 530
0
votes
0
replies
5.8k
views
lncRNA target interaction prediction
lncRNA Target deltaG
8.9 years ago by nazaninhoseinkhan ▴ 530
0
votes
0
replies
1.5k
views
problem of matching one probe to several lncRNA
lncRNA probe matching problem
9.0 years ago by nazaninhoseinkhan ▴ 530
2
votes
4
replies
2.3k
views
A question about RNASeq experiment design
rna-seq experiment design
updated 9.0 years ago by ★ 2.2k • written 9.0 years ago by ▴ 530
0
votes
1
reply
1.9k
views
Finding activation or repression relationships between transcription factors and target genes in human
TF-Target activation or repression
updated 9.0 years ago by ★ 4.0k • written 9.0 years ago by ▴ 530
2
votes
2
replies
3.5k
views
Problem with working with "methAnalysis" package in R
Methylation R methyAnalysis
updated 9.1 years ago by 105k • written 9.1 years ago by ▴ 530
11
votes
4
replies
9.7k
views
False discovery rate
microarray
updated 3.7 years ago by 45k • written 11.0 years ago by ▴ 530
0
votes
3
replies
5.4k
views
Getgeo Error
bioconductor
updated 9.3 years ago by ★ 1.6k • written 11.9 years ago by ▴ 530
0
votes
8
replies
2.5k
views
Difficulty in understanding the experimental design ofa RNASeq project
RNA-Seq
updated 9.3 years ago by ★ 2.1k • written 9.4 years ago by ▴ 530
0
votes
1
reply
2.0k
views
problem in visualizing VCF file (VCFannotation output of Galaxy) in IGV
IGV VCFannotation
updated 9.4 years ago by 20 • written 9.4 years ago by ▴ 530
3
votes
3
replies
2.7k
views
Downloading data from TCGA
TCGA
updated 2.6 years ago by 45k • written 9.4 years ago by ▴ 530
4
votes
9
replies
2.5k
views
8 follow
website for clinical interpretation of NGS data
NGS data Clinical interpretation
updated 9.5 years ago by ▴ 700 • written 9.5 years ago by ▴ 530
2
votes
3
replies
2.7k
views
problem with using CuffMerge in Galaxy
RNASeq Galaxy CuffMerge
updated 9.5 years ago by ▴ 400 • written 9.5 years ago by ▴ 530
1
vote
4
replies
3.1k
views
Difficulty in getting GTF file from iGenomes
RNA-Seq GTF annotation
updated 9.5 years ago by 105k • written 9.5 years ago by ▴ 530
8
votes
14
replies
8.6k
views
aracne in R using minet package
R
updated 2.9 years ago by 45k • written 10.9 years ago by ▴ 530
1
vote
1
reply
2.2k
views
co-expression between transcription factors and their targets
co-expression TFs-target genes
updated 9.7 years ago by 105k • written 9.7 years ago by ▴ 530
0
votes
0
replies
3.2k
views
problem with MinWG installation
alignment bowtie MinWG installation error
9.8 years ago by nazaninhoseinkhan ▴ 530
129 results • Page 2 of 3
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