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Showing :
questions
0
votes
2
replies
705
views
Problem to create count file through HTSeq application
HTSeq
RNA-seq
count
HISAT2
15 months ago by
modarzi
▴ 160
0
votes
2
replies
809
views
how to map peptide to Protein?
protein
Proteomics
peptide
TCGA
15 months ago by
modarzi
▴ 160
0
votes
0
replies
352
views
How does find relative pathway to transfer RNA?
pathway
downstream
tRNA
2.2 years ago by
modarzi
▴ 160
3
votes
3
replies
1.1k
views
how does annotate circular RNA ?
R
Genome
circular
RNA
Position
updated 2.3 years ago by
Barry Digby
★ 1.3k • written 2.3 years ago by
modarzi
▴ 160
7
votes
7
replies
1.9k
views
problem for gene survival analysis through "Survival" package in R
TCGA
Survival Analysis
Gene Survival Analysis
R
updated 2.6 years ago by
huynguyen96.dnu
▴ 50 • written 5.3 years ago by
modarzi
▴ 160
1
vote
2
replies
1.3k
views
how to solve this error when I want to install HISAT2? "E: Unable to locate package hisat2"
hisat2
aligner
2.6 years ago by
modarzi
▴ 160
0
votes
1
reply
567
views
How does find the sequence of each oligonucleotide in microarray probe?
Affymetrics
technology
probe
microarray
updated 2.6 years ago by
cpad0112
21k • written 2.6 years ago by
modarzi
▴ 160
1
vote
3
replies
766
views
how to annotate Circular RNA gene type?
RNA-Seq
Circular RNA
annotation
3.1 years ago by
modarzi
▴ 160
4
votes
5
replies
912
views
should each RNA-seq has Circular RNA?
alignment
RNA-Seq
Circular RNA
CIRI2
written 3.2 years ago by
modarzi
▴ 160
3
votes
5
replies
952
views
problem to aligning FASTQ through BWA aligner
genome
BWA
alignment
updated 3.1 years ago by
andres.firrincieli
3.6k • written 3.1 years ago by
modarzi
▴ 160
2
votes
6
replies
1.1k
views
is "sequence Duplication levels" has bad effect on Alignment process?
bwa
FastQC
RNA-seq
updated 3.2 years ago by
ATpoint
81k • written 3.2 years ago by
modarzi
▴ 160
7
votes
6
replies
1.4k
views
what should be view inside of SAM file?
SAM
BWA
updated 3.2 years ago by
Antonio R. Franco
★ 5.1k • written 3.2 years ago by
modarzi
▴ 160
0
votes
0
replies
846
views
how to find consensus modules between 2 datasets by different platform through WGCNA
WGCNA
consensus module
RNA-seq
microarray
3.4 years ago by
modarzi
▴ 160
1
vote
3
replies
1.4k
views
How can I annotate microarray data set through Ensemble Id?
Affymetrix
Ensemble Id
GPL 96
updated 2.3 years ago by
seta
★ 1.9k • written 3.7 years ago by
modarzi
▴ 160
2
votes
5
replies
1.4k
views
how does find the normalization method in GSE in GEO for microarray data?
MAS 5.0 method
normalization
microarray
3.7 years ago by
modarzi
▴ 160
0
votes
0
replies
874
views
finding AUC and AUCPR in gene regulatory network through ARACNE and CLR methods
AUC
AUCPR
GRN
ARACNE
CKR
3.8 years ago by
modarzi
▴ 160
4
votes
2
replies
1.8k
views
Problem relate to running ClueGO in Cytoscape
Cytoscape
ClueGO
CluePedia
updated 3.9 years ago by
scooter
▴ 620 • written 3.9 years ago by
modarzi
▴ 160
2
votes
12
replies
4.1k
views
Problem for Running "multivariate Cox proportional hazards model"
multivariate Cox
Survival Analysis
cox regression
updated 2.2 years ago by
hakunamatataaa
• 0 • written 4.0 years ago by
modarzi
▴ 160
1
vote
0
replies
744
views
How to use Sex of Patients for Constructing Co-expression Network through WGCNA
RNA-Seq
WGCNA
4.2 years ago by
modarzi
▴ 160
3
votes
4
replies
1.5k
views
which Length of gene is valid for using in Transcript Per million (TPM)?
RNA-Seq
Normalization
TPM
updated 4.3 years ago by
Kevin Blighe
87k • written 4.3 years ago by
modarzi
▴ 160
0
votes
2
replies
1.3k
views
Interpretation problem at PCA plot for detecting batch effect
batch effect
RNA-Seq
PCA
4.3 years ago by
modarzi
▴ 160
4
votes
8
replies
1.2k
views
problem for Collapsing Probes For Same Gene in microarray gene expression data
aggregate
Microarray
Collapsing Probes
4.4 years ago by
modarzi
▴ 160
0
votes
3
replies
2.6k
views
how to measure silhouette coefficient and Dunn index for Hierarchical Clustering in WGCNA?
silhouette coefficient
WGCNA
4.4 years ago by
modarzi
▴ 160
0
votes
0
replies
976
views
problem for merging 2 pairs of reads by "SeqPrep" tool
seqprep
rna-seq
4.4 years ago by
modarzi
▴ 160
1
vote
5
replies
4.5k
views
what does negative value mean in gene expression profile?
RNA-Seq
gene expression
4.4 years ago by
modarzi
▴ 160
1
vote
5
replies
2.2k
views
constructing network by WGCNA and validation Hub genes
Network Construction
WGCNA
hub genes
4.5 years ago by
modarzi
▴ 160
5
votes
5
replies
6.9k
views
Exporting WGCNA step-to-step network construction objects into igraph object
WGCNA
igraph
updated 2.3 years ago by
Karthik
• 0 • written 4.5 years ago by
modarzi
▴ 160
1
vote
0
replies
1.4k
views
finding Topological Overlap Matrix(TOMType) value in TOMsimilarity() function in WGCNA
WGCNA
TOM
updated 4.5 years ago by
Biostar
20 • written 4.7 years ago by
modarzi
▴ 160
0
votes
1
reply
689
views
Problem for downloading Non-coding RNA from Gene Expression Omnibus (GEO)
Non-coding RNA
GEO
4.7 years ago by
modarzi
▴ 160
0
votes
3
replies
1.0k
views
how to filter genes in significant module?
wgcna
significant modules
4.7 years ago by
modarzi
▴ 160
0
votes
0
replies
1.3k
views
how to match Ref. and Test data set genes for module preservation based on WGCNA?
WGCNA
module preservation
4.9 years ago by
modarzi
▴ 160
2
votes
4
replies
1.2k
views
Problem for reading annotation file for GPL10999_family.soft
annotation
5.0 years ago by
modarzi
▴ 160
3
votes
3
replies
1.0k
views
problem for 2 different normalization methods in train and test data set
RNA-Seq
FPKM-UQ
TPM
updated 5.0 years ago by
Charles Warden
8.2k • written 5.0 years ago by
modarzi
▴ 160
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez ID
"org.Dr.eg.db" package
5.4 years ago by
modarzi
▴ 160
1
vote
3
replies
1.0k
views
problem with facing strange gene name in TCGA data
RNA-Seq
TCGA
batch effect correction
updated 5.5 years ago by
Kevin Blighe
87k • written 5.5 years ago by
modarzi
▴ 160
13
votes
15
replies
4.4k
views
Problem for getting P-Value in Module-Trait Relationship in WGCNA
WGCNA
P-Value
Network Analysis
updated 2.6 years ago by
txtbookir
▴ 30 • written 5.6 years ago by
modarzi
▴ 160
14
votes
15
replies
3.6k
views
how to calculate or extract Circular RNA expression via RNA-seq data
RNA-Seq
Circular RNA
updated 5.6 years ago by
abdul.suboor123
• 0 • written 5.8 years ago by
modarzi
▴ 160
9
votes
18
replies
5.5k
views
problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
RNA-Seq
WGCNA
Topological overlap Matrix
updated 5.7 years ago by
WouterDeCoster
47k • written 5.7 years ago by
modarzi
▴ 160
1
vote
2
replies
1.2k
views
problem for finding relative Version GTF file for my .fa file
alignment
Burrows-Wheeler Alignment Tool
5.8 years ago by
modarzi
▴ 160
1
vote
1
reply
983
views
Problem for separating reverse and forward reading in my RNA-seq
RNA-Seq
sequencing
Paired End
5.8 years ago by
modarzi
▴ 160
0
votes
2
replies
2.2k
views
Error in CIRI2 as a circular RNA extracting tool for my data set
RNA-Seq
Circular RNA
CIRI2
updated 5.8 years ago by
archana.bioinfo87
▴ 210 • written 5.9 years ago by
modarzi
▴ 160
2
votes
4
replies
2.3k
views
Problem for understanding the number of modules in construction network based on WGCNA algorithm
WGCNA
Co-expression Network
updated 5.8 years ago by
Jake Warner
▴ 830 • written 5.8 years ago by
modarzi
▴ 160
1
vote
1
reply
1.1k
views
downloading GTF file as gzip format from UCSC website
gene
updated 5.8 years ago by
GenoMax
140k • written 5.8 years ago by
modarzi
▴ 160
5
votes
8
replies
4.2k
views
Error for reading .gtf file in R
Gene Transform Format
GTF
RNA-Seq
refGenome
updated 5.8 years ago by
Kristoffer Vitting-Seerup
★ 4.0k • written 5.9 years ago by
modarzi
▴ 160
1
vote
6
replies
1.3k
views
problem for comparing 2 type of annotation file
gencode
RNA-Seq
TCGA
updated 12 months ago by
Zhenyu Zhang
★ 1.1k • written 5.8 years ago by
modarzi
▴ 160
1
vote
2
replies
981
views
question for Accession No. : SSR
RNA-Seq
SSR
updated 5.9 years ago by
ATpoint
81k • written 5.9 years ago by
modarzi
▴ 160
8
votes
14
replies
5.9k
views
Error in BWA-MEM running in linux
RNA-Seq
BWA-MEM
alignment
updated 5.9 years ago by
GenoMax
140k • written 5.9 years ago by
modarzi
▴ 160
0
votes
4
replies
1.8k
views
problem in running CIRI2 as a circular RNA extracting tool
RNA-Seq
Circular RNA
updated 5.9 years ago by
GenoMax
140k • written 5.9 years ago by
modarzi
▴ 160
1
vote
3
replies
1.6k
views
problem for setting BWA arguments for alignment
RNA-Seq
sequencing
alignment
BWA
updated 5.9 years ago by
Tm
★ 1.1k • written 5.9 years ago by
modarzi
▴ 160
5
votes
12
replies
4.8k
views
data pre-processing for WGCNA Algorithm
RNA-Seq
WGCNA
Pre-processing
FPKM
TCGA
updated 5.9 years ago by
Kevin Blighe
87k • written 5.9 years ago by
modarzi
▴ 160
57 results • Page
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