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2
votes
3
replies
522
views
Problem in removing batch effect by DeSeq2
removing effects DeSeq2 batch colData
updated 10 months ago by 77k • written 10 months ago by ▴ 510
0
votes
2
replies
399
views
Can a pathogenic mutation results in the up-regulation of a gene?
mutation-up-regulation Pathogenic
16 months ago by nazaninhoseinkhan ▴ 510
0
votes
0
replies
360
views
"read error; binarycodec in readmode" error in HMMRATAC
BAM HMMRATAC
updated 4 months ago by 40k • written 21 months ago by ▴ 510
0
votes
0
replies
301
views
How can I get plate information for a single cell sequencing dataset
sequencing cell single plate information
23 months ago by nazaninhoseinkhan ▴ 510
3
votes
3
replies
723
views
Why only reverse fatsq file is used for mapping step in single cell RNA sequencing analysis?
ScRNA-Seq
updated 6 months ago by 40k • written 23 months ago by ▴ 510
0
votes
1
reply
430
views
EnsemblVEP could not generate any output for a list of frameshift insertion input
Frame_Shift_Insertion EnsemblVEP
2.2 years ago by nazaninhoseinkhan ▴ 510
0
votes
3
replies
1.6k
views
conversion of case_ids to file_ids TCGA data
TCGA case_ids conversion
updated 2.2 years ago by • 0 • written 4.3 years ago by ▴ 510
0
votes
2
replies
629
views
Matching the file names with exposure file in TCGA
FPKM exposure TCGA
updated 6 months ago by 40k • written 2.2 years ago by ▴ 510
7
votes
18
replies
4.9k
views
problem in matching the names between file names and patients Id in TCGA
TCGA CNV problem in matching
updated 2.6 years ago by ▴ 30 • written 5.3 years ago by ▴ 510
0
votes
1
reply
2.0k
views
module membership p-value cutoff
wgcna module membership p-value cutoff
updated 2.6 years ago by 20 • written 6.0 years ago by ▴ 510
26
votes
57
replies
7.0k
views
how to generate CNV plot from VEP results
copy number alteration VEP CNV plot
updated 2.8 years ago by 40k • written 5.0 years ago by ▴ 510
1
vote
6
replies
1.1k
views
Methylation-Gene expression correlation
DNA methylation Gene expression Correlation
updated 3.1 years ago by 86k • written 3.1 years ago by ▴ 510
0
votes
3
replies
1.2k
views
visualizing mutational data using Maftools for reference genome hg19
hg19 visualize Maftools SNV
3.1 years ago by nazaninhoseinkhan ▴ 510
2
votes
2
replies
1.9k
views
How to find targets for large number of lncRNAs
lncRNA targets
updated 3.3 years ago by 20 • written 7.0 years ago by ▴ 510
1
vote
18
replies
2.1k
views
Negative gene expression values in "Illumina HumanHT-12 WG-DASL V4.0 R2 expression beadchip"
Negative expression values
updated 3.4 years ago by 86k • written 3.4 years ago by ▴ 510
2
votes
3
replies
624
views
several copy number alterations in the same position in an individual
SCNA
updated 3.4 years ago by 40k • written 3.4 years ago by ▴ 510
3
votes
12
replies
981
views
MUC5AC is not present in deseq2 results
RNA-Seq Deseq2 MUC5AC
3.5 years ago by nazaninhoseinkhan ▴ 510
0
votes
0
replies
917
views
How to specify pipelines(muse, mutect,...) in TCGAbiolinks when you want to use hg19?
TCGAbiolinks mutations pipelines selection hg19
3.7 years ago by nazaninhoseinkhan ▴ 510
2
votes
3
replies
687
views
What should I do when some probes of a gene is detected as hypomethylated and other probes of the same gene is hypermethylated
DNA methylation hyper-hypomethyaltion same gene
3.7 years ago by nazaninhoseinkhan ▴ 510
0
votes
0
replies
466
views
problem in finding follow_up samples belong to the same patients in TCGA
TCGA codes follow_up samples
3.8 years ago by nazaninhoseinkhan ▴ 510
6
votes
6
replies
900
views
No mutations or copy number alterations was detected in stage I of cancer
SNP copy number alteration stage one tumor
3.8 years ago by nazaninhoseinkhan ▴ 510
0
votes
2
replies
922
views
Problem in matching "days_to_last_followup" to the sample IDs in TCGA clinical files
TCGA Clinical file
3.9 years ago by nazaninhoseinkhan ▴ 510
0
votes
1
reply
558
views
How to make a representative copy number variation sample from several samples based on their overlaps?
Copy number variations getting overlaps
updated 3.9 years ago by ★ 15k • written 3.9 years ago by ▴ 510
0
votes
0
replies
748
views
Unable to find normal samples in TCGA Esoghagus cancer samples
TCGA Esophagus caner normal (nontumorous)
3.9 years ago by nazaninhoseinkhan ▴ 510
2
votes
16
replies
1.3k
views
how to get copy number alteration results for each patients?
CNA result for each individual patient
updated 4.0 years ago by 86k • written 4.0 years ago by ▴ 510
0
votes
3
replies
2.1k
views
Methylation analysis using TCGAbiolinks package
TCGAbiolinks methylation
updated 4.2 years ago by ▴ 50 • written 4.4 years ago by ▴ 510
3
votes
3
replies
2.8k
views
The proper order of defining groups in GEO2R
GEO2R order of defining groups
updated 4.4 years ago by ▴ 10 • written 5.7 years ago by ▴ 510
0
votes
0
replies
669
views
How to analyze Geniom Biochips Microarray data
Geniom Biochip arrayExpress normalization
4.4 years ago by nazaninhoseinkhan ▴ 510
0
votes
2
replies
1.2k
views
how to define different batches in DESeq2 in Galaxy
RNA-Seq DESeq2 batch effect removal
updated 4.5 years ago by 20 • written 5.3 years ago by ▴ 510
0
votes
0
replies
887
views
How to define groups for dual channel microarray data in GEO2R?
GEO2R dual channel define groups
4.6 years ago by nazaninhoseinkhan ▴ 510
0
votes
1
reply
1.1k
views
Rarefaction curves does not show all sample curves
Metagenomic analysis Rarefaction.single
4.7 years ago by nazaninhoseinkhan ▴ 510
2
votes
3
replies
1.6k
views
Reading TCGA methylation .txt files in R
Methylation analysis TCGA
4.8 years ago by nazaninhoseinkhan ▴ 510
2
votes
2
replies
843
views
Hierarchical clustering to group large number of samples
RNA-Seq sample clustering
updated 4.8 years ago by 26k • written 4.8 years ago by ▴ 510
1
vote
9
replies
2.7k
views
7 follow
Differential expression analysis on miRNA count files
mirSeq Differential expression
updated 4.8 years ago by ▴ 760 • written 4.9 years ago by ▴ 510
0
votes
0
replies
1.2k
views
problem in interpretation of Gistic copy number analysis
copy number alteration Gistic G-score
5.0 years ago by nazaninhoseinkhan ▴ 510
4
votes
2
replies
1.5k
views
absence of gene symbol when selecting "most severe consequence" in VEP
Variant Effect Predictor filtering
updated 5.0 years ago by 23k • written 5.0 years ago by ▴ 510
0
votes
1
reply
890
views
Discrepancy in Copy Number Alteration between different cancer stages
copy number alteration cancer stages
updated 5.0 years ago by ▴ 840 • written 5.0 years ago by ▴ 510
4
votes
4
replies
6.3k
views
ClusterProfiler cannot map any gene
clusterProfiler EnsemblIDs biomaRt
5.0 years ago by nazaninhoseinkhan ▴ 510
0
votes
6
replies
1.7k
views
problem in getting results from variant effect predictor(VEP)
VEP online error message
5.1 years ago by nazaninhoseinkhan ▴ 510
3
votes
5
replies
940
views
changing the pattern of expression in two sequential stages of cancer
cancer stages converse pattern of expression
updated 5.1 years ago by 86k • written 5.1 years ago by ▴ 510
2
votes
10
replies
2.2k
views
problem with using gtf file in cufflinks in Galaxy
RNA-Seq GTF Cufflinks FPKM
updated 5.1 years ago by 20 • written 7.4 years ago by ▴ 510
4
votes
2
replies
1.3k
views
Copy number variation between different cancer stages
CNV analysis different cancer stages
updated 5.1 years ago by 86k • written 5.1 years ago by ▴ 510
19
votes
43
replies
4.7k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.1 years ago by nazaninhoseinkhan ▴ 510
2
votes
8
replies
2.1k
views
no significant FDR in gene enrichment analysis
rna-seq DEGs enrichment FDR
5.2 years ago by nazaninhoseinkhan ▴ 510
3
votes
5
replies
3.6k
views
removing outliers before running DESeq2
RNA-Seq outliers deseq2
updated 5.2 years ago by 3.2k • written 5.2 years ago by ▴ 510
2
votes
6
replies
5.8k
views
what logFC or adj-p value cutoff should be chosen when the number of samples in one of the conditions is too small?
RNA-Seq DESeq2 small number of normal samples
updated 5.2 years ago by 86k • written 5.2 years ago by ▴ 510
0
votes
2
replies
1.6k
views
Illumina BeadChip Array probe file Vs control probe file
Illumina BeadChip Array Control probe file
updated 5.2 years ago by 20 • written 5.4 years ago by ▴ 510
12
votes
13
replies
4.4k
views
6 follow
problem in EnsemblID to gene symbol conversion in TCGA data
RNA-Seq TCGA read counts ensembl
updated 13 months ago by ▴ 80 • written 5.3 years ago by ▴ 510
2
votes
5
replies
1.6k
views
what TCGA biospecimen filter should be selected for retrieving "invasive ductal breast carcinoma" data?
TCGA invasive ductal carcinoma
5.3 years ago by nazaninhoseinkhan ▴ 510
2
votes
5
replies
2.4k
views
Is it correct if we use htseq counts as raw read counts in DESEq2?
RNA-Seq DESeq2 htseqCounts
updated 5.3 years ago by 103k • written 5.3 years ago by ▴ 510
127 results • Page 1 of 3
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