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1
vote
2
replies
356
views
Problem with survival analysis with gene symbols containing hyphen
R Survival-analysis
3 months ago by nazaninhoseinkhan ▴ 520
2
votes
3
replies
743
views
Problem in removing batch effect by DeSeq2
removing effects DeSeq2 batch colData
updated 18 months ago by 82k • written 18 months ago by ▴ 520
0
votes
2
replies
523
views
Can a pathogenic mutation results in the up-regulation of a gene?
mutation-up-regulation Pathogenic
24 months ago by nazaninhoseinkhan ▴ 520
0
votes
0
replies
457
views
"read error; binarycodec in readmode" error in HMMRATAC
BAM HMMRATAC
updated 12 months ago by 43k • written 2.3 years ago by ▴ 520
0
votes
0
replies
391
views
How can I get plate information for a single cell sequencing dataset
sequencing cell single plate information
2.5 years ago by nazaninhoseinkhan ▴ 520
3
votes
3
replies
914
views
Why only reverse fatsq file is used for mapping step in single cell RNA sequencing analysis?
ScRNA-Seq
updated 14 months ago by 43k • written 2.5 years ago by ▴ 520
0
votes
1
reply
535
views
EnsemblVEP could not generate any output for a list of frameshift insertion input
Frame_Shift_Insertion EnsemblVEP
2.8 years ago by nazaninhoseinkhan ▴ 520
0
votes
3
replies
1.8k
views
conversion of case_ids to file_ids TCGA data
TCGA case_ids conversion
updated 2.8 years ago by • 0 • written 5.0 years ago by ▴ 520
0
votes
2
replies
783
views
Matching the file names with exposure file in TCGA
FPKM exposure TCGA
updated 14 months ago by 43k • written 2.9 years ago by ▴ 520
7
votes
18
replies
5.6k
views
problem in matching the names between file names and patients Id in TCGA
TCGA CNV problem in matching
updated 3.2 years ago by ▴ 30 • written 5.9 years ago by ▴ 520
0
votes
1
reply
2.1k
views
module membership p-value cutoff
wgcna module membership p-value cutoff
updated 3.2 years ago by 20 • written 6.7 years ago by ▴ 520
26
votes
57
replies
8.5k
views
how to generate CNV plot from VEP results
copy number alteration VEP CNV plot
updated 3.4 years ago by 43k • written 5.6 years ago by ▴ 520
1
vote
6
replies
1.3k
views
Methylation-Gene expression correlation
DNA methylation Gene expression Correlation
updated 3.7 years ago by 88k • written 3.7 years ago by ▴ 520
1
vote
3
replies
1.4k
views
visualizing mutational data using Maftools for reference genome hg19
hg19 visualize Maftools SNV
3.7 years ago by nazaninhoseinkhan ▴ 520
2
votes
2
replies
2.1k
views
How to find targets for large number of lncRNAs
lncRNA targets
updated 4.0 years ago by 20 • written 7.7 years ago by ▴ 520
1
vote
18
replies
2.6k
views
Negative gene expression values in "Illumina HumanHT-12 WG-DASL V4.0 R2 expression beadchip"
Negative expression values
updated 4.0 years ago by 88k • written 4.0 years ago by ▴ 520
2
votes
3
replies
775
views
several copy number alterations in the same position in an individual
SCNA
updated 4.0 years ago by 43k • written 4.1 years ago by ▴ 520
3
votes
12
replies
1.3k
views
MUC5AC is not present in deseq2 results
RNA-Seq Deseq2 MUC5AC
4.1 years ago by nazaninhoseinkhan ▴ 520
0
votes
0
replies
1.0k
views
How to specify pipelines(muse, mutect,...) in TCGAbiolinks when you want to use hg19?
TCGAbiolinks mutations pipelines selection hg19
4.3 years ago by nazaninhoseinkhan ▴ 520
2
votes
3
replies
861
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
4.4 years ago by nazaninhoseinkhan ▴ 520
0
votes
0
replies
531
views
problem in finding follow_up samples belong to the same patients in TCGA
TCGA codes follow_up samples
4.4 years ago by nazaninhoseinkhan ▴ 520
6
votes
6
replies
1.1k
views
No mutations or copy number alterations was detected in stage I of cancer
SNP copy number alteration stage one tumor
4.4 years ago by nazaninhoseinkhan ▴ 520
0
votes
2
replies
1.1k
views
Problem in matching "days_to_last_followup" to the sample IDs in TCGA clinical files
TCGA Clinical file
4.5 years ago by nazaninhoseinkhan ▴ 520
0
votes
1
reply
647
views
How to make a representative copy number variation sample from several samples based on their overlaps?
Copy number variations getting overlaps
updated 4.5 years ago by ★ 16k • written 4.5 years ago by ▴ 520
0
votes
0
replies
840
views
Unable to find normal samples in TCGA Esoghagus cancer samples
TCGA Esophagus caner normal (nontumorous)
4.6 years ago by nazaninhoseinkhan ▴ 520
2
votes
16
replies
1.7k
views
how to get copy number alteration results for each patients?
CNA result for each individual patient
updated 4.6 years ago by 88k • written 4.6 years ago by ▴ 520
0
votes
3
replies
2.2k
views
Methylation analysis using TCGAbiolinks package
TCGAbiolinks methylation
updated 4.8 years ago by ▴ 50 • written 5.0 years ago by ▴ 520
4
votes
3
replies
3.1k
views
The proper order of defining groups in GEO2R
GEO2R order of defining groups
updated 5.0 years ago by ▴ 20 • written 6.4 years ago by ▴ 520
0
votes
0
replies
741
views
How to analyze Geniom Biochips Microarray data
Geniom Biochip arrayExpress normalization
5.0 years ago by nazaninhoseinkhan ▴ 520
0
votes
2
replies
1.4k
views
how to define different batches in DESeq2 in Galaxy
RNA-Seq DESeq2 batch effect removal
updated 5.1 years ago by 20 • written 5.9 years ago by ▴ 520
0
votes
0
replies
988
views
How to define groups for dual channel microarray data in GEO2R?
GEO2R dual channel define groups
5.2 years ago by nazaninhoseinkhan ▴ 520
0
votes
1
reply
1.2k
views
Rarefaction curves does not show all sample curves
Metagenomic analysis Rarefaction.single
5.3 years ago by nazaninhoseinkhan ▴ 520
2
votes
3
replies
1.8k
views
Reading TCGA methylation .txt files in R
Methylation analysis TCGA
5.4 years ago by nazaninhoseinkhan ▴ 520
2
votes
2
replies
957
views
Hierarchical clustering to group large number of samples
RNA-Seq sample clustering
updated 5.4 years ago by 27k • written 5.4 years ago by ▴ 520
1
vote
9
replies
3.1k
views
7 follow
Differential expression analysis on miRNA count files
mirSeq Differential expression
updated 5.4 years ago by ▴ 800 • written 5.5 years ago by ▴ 520
0
votes
0
replies
1.3k
views
problem in interpretation of Gistic copy number analysis
copy number alteration Gistic G-score
5.6 years ago by nazaninhoseinkhan ▴ 520
5
votes
2
replies
1.7k
views
absence of gene symbol when selecting "most severe consequence" in VEP
Variant Effect Predictor filtering
updated 5.6 years ago by 23k • written 5.6 years ago by ▴ 520
0
votes
1
reply
993
views
Discrepancy in Copy Number Alteration between different cancer stages
copy number alteration cancer stages
updated 5.6 years ago by ▴ 850 • written 5.6 years ago by ▴ 520
4
votes
4
replies
7.0k
views
ClusterProfiler cannot map any gene
clusterProfiler EnsemblIDs biomaRt
5.7 years ago by nazaninhoseinkhan ▴ 520
0
votes
6
replies
1.9k
views
problem in getting results from variant effect predictor(VEP)
VEP online error message
5.7 years ago by nazaninhoseinkhan ▴ 520
3
votes
5
replies
1.1k
views
changing the pattern of expression in two sequential stages of cancer
cancer stages converse pattern of expression
updated 5.7 years ago by 88k • written 5.7 years ago by ▴ 520
2
votes
10
replies
2.4k
views
problem with using gtf file in cufflinks in Galaxy
RNA-Seq GTF Cufflinks FPKM
updated 5.7 years ago by 20 • written 8.0 years ago by ▴ 520
4
votes
2
replies
1.4k
views
Copy number variation between different cancer stages
CNV analysis different cancer stages
updated 5.7 years ago by 88k • written 5.7 years ago by ▴ 520
19
votes
43
replies
5.6k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.7 years ago by nazaninhoseinkhan ▴ 520
2
votes
8
replies
2.3k
views
no significant FDR in gene enrichment analysis
rna-seq DEGs enrichment FDR
5.8 years ago by nazaninhoseinkhan ▴ 520
3
votes
5
replies
4.0k
views
removing outliers before running DESeq2
RNA-Seq outliers deseq2
updated 5.8 years ago by 3.2k • written 5.8 years ago by ▴ 520
3
votes
6
replies
6.5k
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 5.8 years ago by 88k • written 5.8 years ago by ▴ 520
0
votes
2
replies
1.8k
views
Illumina BeadChip Array probe file Vs control probe file
Illumina BeadChip Array Control probe file
updated 5.9 years ago by 20 • written 6.1 years ago by ▴ 520
12
votes
13
replies
5.1k
views
6 follow
problem in EnsemblID to gene symbol conversion in TCGA data
RNA-Seq TCGA read counts ensembl
updated 20 months ago by ▴ 90 • written 5.9 years ago by ▴ 520
2
votes
5
replies
1.7k
views
what TCGA biospecimen filter should be selected for retrieving "invasive ductal breast carcinoma" data?
TCGA invasive ductal carcinoma
5.9 years ago by nazaninhoseinkhan ▴ 520
128 results • Page 1 of 3
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