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0
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192
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Tools for network alignement
graph network R netcom igraph
updated 12 weeks ago by 43k • written 12 weeks ago by ▴ 510
1
vote
1
reply
512
views
Network cross-validation
wgcna RNASeq Network CV
updated 10 months ago by 3.9k • written 10 months ago by ▴ 510
3
votes
3
replies
832
views
Log fold change from rlog
logarithms R deseq
updated 18 months ago by 82k • written 18 months ago by ▴ 510
1
vote
1
reply
955
views
RRBS data analysis using Bismark and methylkit
RRBS methylkit Bismark WGBS
updated 2.6 years ago by ★ 2.9k • written 2.6 years ago by ▴ 510
2
votes
3
replies
805
views
Contigs and scaffold in reference genome
BWA Ensembl Genome Reference HiSat NCBI
updated 2.8 years ago by 141k • written 2.8 years ago by ▴ 510
0
votes
0
replies
692
views
Read trimming in BS-Seq
Methylation BS-Seq Bismark WGBS
2.9 years ago by Arindam Ghosh ▴ 510
0
votes
0
replies
1.4k
views
Bismark to MethylKit
methylkit bismark bsseq
2.9 years ago by Arindam Ghosh ▴ 510
1
vote
1
reply
969
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Pathway network
Reactome Pathway cytoscape KEGG igraph
updated 3.0 years ago by 27k • written 3.0 years ago by ▴ 510
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0
replies
456
views
Is there a limit on the number of query in cir_query()?
R SMILES webchem
3.0 years ago by Arindam Ghosh ▴ 510
0
votes
0
replies
2.0k
views
HiSat2 vs BowTie2 for mapping miRNA-seq reads
miRNA-Seq Hisat2 Bowtie
updated 3.4 years ago by 20 • written 3.8 years ago by ▴ 510
57
votes
22
replies
28k
views
7 follow
Batch correction in DESeq2
Combat DESeq2 Batch-Effect
updated 21 days ago by 43k • written 4.5 years ago by ▴ 510
2
votes
8
replies
2.7k
views
Full GTF file vs Subset GTF file
featurecounts RNA-Seq miRNA-seq Ensembl
updated 3.8 years ago by ▴ 520 • written 3.8 years ago by ▴ 510
2
votes
2
replies
1.3k
views
Annotation for miRNA-seq data analysis
mirna hisat ensembl RNA-Seq Assembly
updated 3.8 years ago by ▴ 330 • written 3.8 years ago by ▴ 510
1
vote
2
replies
847
views
How to identify ZNFs from a gene list?
protein domain pfam uniprot
updated 4.1 years ago by 161k • written 4.1 years ago by ▴ 510
1
vote
1
reply
1.2k
views
Compact visualisation of enrichment analysis
RNA-Seq gene ontology PANTHER DAVID REVIGO
updated 4.2 years ago by ★ 2.6k • written 4.2 years ago by ▴ 510
0
votes
0
replies
632
views
Signed hybrid network vs up/down -reg network
WGCNA network
4.3 years ago by Arindam Ghosh ▴ 510
2
votes
3
replies
3.3k
views
What is the need for signed or signed hybrid (as in WGCNA) co-expression networks?
wgcna network
updated 4.4 years ago by 3.6k • written 4.4 years ago by ▴ 510
2
votes
1
reply
1.6k
views
Threshold in WGCNA
RNA-Seq wgcna
4.5 years ago by Arindam Ghosh ▴ 510
7
votes
2
replies
9.5k
views
What is a good Trimmomatic parameter?
trimmomatic RNA-Seq ngs sequencing
updated 4.6 years ago by ▴ 10 • written 6.0 years ago by ▴ 510
13
votes
13
replies
18k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq FastQC QC GC-content
4.7 years ago by Arindam Ghosh ▴ 510
4
votes
2
replies
3.1k
views
How to efetch specific attributes from BioSamples?
ncbi eutils xml
updated 5.2 years ago by 161k • written 5.2 years ago by ▴ 510
2
votes
2
replies
1.5k
views
What does cluster number in ClusterMaker represent?
cytoscape clustering clustermaker network
updated 5.2 years ago by ▴ 620 • written 5.2 years ago by ▴ 510
2
votes
3
replies
1.3k
views
How to construct GCN?
RNA-Seq network gene coexpression network
updated 5.3 years ago by 87k • written 5.3 years ago by ▴ 510
0
votes
1
reply
3.5k
views
What are the terms to look forward to for proper equilibration in GROMACS?
gromacs molecular dynamics
updated 5.5 years ago by ▴ 10 • written 6.2 years ago by ▴ 510
13
votes
8
replies
9.3k
views
How to graphically tell if data has been normalized?
DESeq2 RNA-Seq normalization
updated 5.8 years ago by 87k • written 5.8 years ago by ▴ 510
2
votes
7
replies
3.0k
views
What if a network is not scale-free?
network cytoscape RNA-Seq
5.8 years ago by Arindam Ghosh ▴ 510
12
votes
19
replies
3.9k
views
6 follow
How many genes in RNA seq?
RNA-Seq stringtie
5.9 years ago by Arindam Ghosh ▴ 510
2
votes
8
replies
2.1k
views
6 follow
Which HTSeq mode is suitable for RNAseq data to be used for differential gene expression?
RNA-Seq alignment ngs
updated 5.9 years ago by 35k • written 5.9 years ago by ▴ 510
0
votes
0
replies
3.4k
views
What is a good binding energy in AutoDock?
docking autodock protein
6.0 years ago by Arindam Ghosh ▴ 510
0
votes
2
replies
2.9k
views
Code for DEG analysis using Ballgown
RNA-Seq ballgown stattest ngs
updated 6.0 years ago by 5.8k • written 6.1 years ago by ▴ 510
3
votes
11
replies
4.6k
views
How to calculate fold change?
RNA-Seq ngs statistics R
updated 6.1 years ago by 104k • written 6.1 years ago by ▴ 510
5
votes
2
replies
3.0k
views
What is the difference between gene FPKM and transcript FPKM values?
RNA-Seq
6.1 years ago by Arindam Ghosh ▴ 510
6
votes
4
replies
2.1k
views
How to sort genes into coding and non-coding mRNA?
RNA-Seq gene sequencing
updated 6.1 years ago by 35k • written 6.1 years ago by ▴ 510
0
votes
1
reply
2.0k
views
Source of bed file
RNA-Seq bed ngs
updated 6.2 years ago by 104k • written 6.2 years ago by ▴ 510
9
votes
7
replies
3.8k
views
7 follow
Are 2 replicates per sample sufficient for RNA-seq data analysis?
RNA-Seq R Ngs
6.2 years ago by Arindam Ghosh ▴ 510
3
votes
1
reply
2.7k
views
Can we directly correlate FPKM/TPM to expression?
RNA-Seq sequencing expession
updated 6.2 years ago by ▴ 330 • written 6.2 years ago by ▴ 510
3
votes
3
replies
3.5k
views
RNA-seq adaptor sequence
RNA-Seq ngs next-gen
updated 6.2 years ago by 35k • written 6.2 years ago by ▴ 510
9
votes
11
replies
1.4k
views
Shifting from microarray to RNAseq
RNA-Seq ngs microarray
updated 6.4 years ago by 8.9k • written 6.4 years ago by ▴ 510
2
votes
9
replies
7.0k
views
Requirements for running HISAT2
ngs RNA-Seq hisat indexing
6.4 years ago by Arindam Ghosh ▴ 510
4
votes
5
replies
1.5k
views
Data selection for RNA-seq data analysis
RNA-Seq ngs data
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by ▴ 510
1
vote
2
replies
1.5k
views
Perl code for counting number of bases
perl coding
updated 6.4 years ago by ★ 3.0k • written 6.4 years ago by ▴ 510
3
votes
4
replies
1.5k
views
How to know if an SRA data contains ERCC spike-in?
RNA-Seq sequencing ngs
updated 6.5 years ago by 104k • written 6.5 years ago by ▴ 510
0
votes
1
reply
1.8k
views
How to create *.dist file?
sequence mothur distance matrix phylogenetics
updated 6.5 years ago by ▴ 200 • written 7.8 years ago by ▴ 510
8
votes
7
replies
2.9k
views
Which is a good source to download a reference genome?
rna-seq genome
updated 6.5 years ago by ▴ 270 • written 6.5 years ago by ▴ 510
1
vote
3
replies
1.4k
views
Is it a good idea to proceed with incomplete protein model?
modelling protein structure itasser phyre
6.5 years ago by Arindam Ghosh ▴ 510
19
votes
9
replies
28k
views
7 follow
Can anyone suggest a good tutorial to learn RNA-seq analysis?
analysis RNA-Seq ngs
updated 11 months ago by 43k • written 6.5 years ago by ▴ 510
0
votes
5
replies
2.5k
views
Reference genome for BOWTIE2
RNA-Seq bowtie ngs genome
updated 6.5 years ago by 5.3k • written 6.5 years ago by ▴ 510
0
votes
0
replies
1.9k
views
Error in MDS of complex
Gromacs complex energy minimization
7.1 years ago by Arindam Ghosh ▴ 510
1
vote
3
replies
1.8k
views
16s rRNA gene diversity analysis
mothur metagenomics sequencing 16s
7.8 years ago by Arindam Ghosh ▴ 510
0
votes
1
reply
1.6k
views
in silico study of antimicrobial peptide
simulation peptide antimicrobial gromacs
updated 7.9 years ago by 20 • written 8.0 years ago by ▴ 510
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