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1,000 results • Page
4 of 20
Sort: Views
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Views
Votes
Replies
12
votes
4
replies
2.3k
views
long read + salmon? (transcript abundance)
long-read
salmon
updated 23 days ago by
Ram
43k • written 14 months ago by
shinyjj
▴ 50
2
votes
1
reply
2.3k
views
TCGA RNAseqV2 data matrix batch effect control and remove
RNA-Seq
batch-effect
updated 10 days ago by
Ram
43k • written 7.6 years ago by
fractal61
▴ 10
0
votes
4
replies
2.3k
views
Remove Gaps from Multiple sequence alignment
python
MSA
updated 26 days ago by
Ram
43k • written 2.5 years ago by
ramsha
• 0
2
votes
4
replies
2.2k
views
Negative values after batch correction using removeBatchEffect from Limma
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 12 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
9
votes
5
replies
2.2k
views
Millions of Reads Needed for Differential Gene Expression
differential-gene-expression
RNA-Seq
deseq2
updated 19 days ago by
Ram
43k • written 4.6 years ago by
contact
▴ 20
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 11 days ago by
jakobjung
• 0 • written 4.6 years ago by
adhirajnath14
▴ 40
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq
batch-effect
Random-Forest
updated 11 days ago by
Ram
43k • written 4.7 years ago by
Vlad
▴ 10
5
votes
4
replies
2.2k
views
How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
read-counts
DESEQ2
differential-gene-expression
kallisto
updated 19 days ago by
Ram
43k • written 2.7 years ago by
mrj
▴ 170
4
votes
3
replies
2.2k
views
The result of differential gene expression analysis should be extracted based on adj.p.value ?
limma
microarray
bioconductor
R
updated 11 days ago by
Ram
43k • written 6.3 years ago by
Raheleh
▴ 260
2
votes
5
replies
2.2k
views
Generating a heatmap in DEG analysis
Differential-gene-expression
RNA-Seq
updated 19 days ago by
Ram
43k • written 3.1 years ago by
Pranathi
▴ 10
3
votes
1
reply
2.2k
views
Maximum Number of Gene in a DESeq2 and edgeR
Differential-Gene-Expression
EdgeR
DESeq2
updated 19 days ago by
Ram
43k • written 8.1 years ago by
rieza.aprianto
▴ 10
2
votes
2
replies
2.1k
views
How to use pacbio reads to join contigs
assembly
tgs
pacbio
updated 23 days ago by
Ram
43k • written 6.0 years ago by
934963534
▴ 20
5
votes
5
replies
2.1k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq
tophat
batch-effect
cufflinks
updated 11 days ago by
Ram
43k • written 5.3 years ago by
yff
• 0
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 10 days ago by
Ram
43k • written 4.8 years ago by
BioLite
▴ 20
1
vote
0
replies
2.1k
views
Tool:
DASC -- detecting hidden batch effects in gene expression datasets (Array/RNA-Seq/scRNA-Seq)
RNA-Seq
scRNA-Seq
R
Batch-Effect
updated 10 days ago by
Ram
43k • written 6.9 years ago by
Ar
★ 1.1k
2
votes
3
replies
2.1k
views
Why the PCA results of PCASamples() from methylkit is different from prcomp()?
methylkit
prcomp
pca
PCASamples
multiplePCA
updated 22 days ago by
1769mkc
★ 1.2k • written 4.2 years ago by
maria2019
▴ 250
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna
RNA-Seq
ChIP-Seq
updated 20 days ago by
mflab
• 0 • written 3.9 years ago by
m.sadman.sakib
▴ 120
1
vote
2
replies
2.1k
views
RNA-seq unbalanced batch effect correction
RNA-Seq
edgeR
R
Batch-Effect
updated 11 days ago by
Ram
43k • written 5.6 years ago by
sckinta
▴ 730
3
votes
2
replies
2.1k
views
Batch effect correction - miRNA sequencing - DESeq2
Batch-effect
DESeq2
miRNA-Seq
updated 11 days ago by
Ram
43k • written 5.5 years ago by
prekrish
• 0
3
votes
5
replies
2.1k
views
DE analysis with edgeR and possibly batch effect
analysis
edgeR
batch-effect
DE
updated 11 days ago by
Ram
43k • written 5.1 years ago by
seta
★ 1.9k
0
votes
0
replies
2.1k
views
betweenLaneNormalization and calcNormFactors in RUVs
Differential-Gene-Expression
RUVs
RNA-Seq
R
updated 19 days ago by
Ram
43k • written 6.9 years ago by
manish20072013
▴ 10
1
vote
6
replies
2.1k
views
DGE on protein-coding and lncRNAs separately?
differential-gene-expression
RNA-seq
updated 19 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation
RNA-Seq
R
updated 11 days ago by
Ram
43k • written 6.1 years ago by
mannoulag1
▴ 120
0
votes
5
replies
2.1k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq
batch-effect
normalization
updated 12 days ago by
Ram
43k • written 21 months ago by
mmitra
▴ 60
1
vote
3
replies
2.0k
views
gene expression data analysis and batch effect methods
microarray
Gene-expression
batch-effect
updated 10 days ago by
Ram
43k • written 6.9 years ago by
Shamim Sarhadi
▴ 220
0
votes
0
replies
2.0k
views
NOISeq Batch Correction to RNA-seq data
Batch-effect
RNA-Seq
ARSyNseq
limma
NOISeq
updated 10 days ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
4
votes
6
replies
2.0k
views
RNA-Seq DGE: Evaluate model quality
differential-gene-expression
RNA-Seq
deseq2
updated 19 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
0
votes
1
reply
2.0k
views
Is it appropriate to apply RUVseq on output from kallisto?
RNA-Seq
batch-correction
kallisto
updated 12 days ago by
Ram
43k • written 5.3 years ago by
unawaz
▴ 60
0
votes
0
replies
2.0k
views
Job:
Bioinformatics Research Postdoc
RNA-Seq
genome
updated 17 days ago by
Ram
43k • written 8.2 years ago by
ggrant543
• 0
0
votes
4
replies
2.0k
views
Requesting help with RNA-Seq differential gene analysis
differential-gene-expression
deseq2
updated 19 days ago by
Ram
43k • written 6.2 years ago by
sagnik
▴ 50
0
votes
0
replies
1.9k
views
Correcting batch effect from known variables in RnBeads using Combat
Combat
450k
methylation
RnBeads
batch-effect
updated 10 days ago by
Ram
43k • written 7.1 years ago by
rahel14350
▴ 40
0
votes
0
replies
1.9k
views
batch effect in radseq
radseq
batch-effect
SNP
updated 10 days ago by
Ram
43k • written 7.5 years ago by
oselm
▴ 50
9
votes
4
replies
1.9k
views
Integration of RNA-Seq data with microarray data
microarray
RNA-Seq
batch-effect
R
updated 12 days ago by
Ram
43k • written 4.0 years ago by
Fahimeh.6868
▴ 30
3
votes
6
replies
1.9k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 2 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
4
votes
5
replies
1.9k
views
which package should be selected for differential gene expression analysis
Differential-gene-expression
RNA-Seq
updated 19 days ago by
Ram
43k • written 5.5 years ago by
lkianmehr
▴ 100
2
votes
5
replies
1.9k
views
Differential Expression Analysis with batches which have different biological groups
R
RNA-Seq
limma
DE
batch-effect
updated 11 days ago by
Ram
43k • written 4.8 years ago by
asalimih
▴ 60
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 23 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 1.9k
7
votes
4
replies
1.9k
views
AlphaFold 2 alternatives
protein-structure
alphafold
updated 26 days ago by
Ram
43k • written 17 months ago by
Dunois
★ 2.5k
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 10 days ago by
Ram
43k • written 6.6 years ago by
Alternative
▴ 270
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression
TPM
RNA-Seq
counts
batch-effect
11 days ago by
Ram
43k
0
votes
7
replies
1.9k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering
dendrogram
RNA-Seq
batch-effect
updated 10 days ago by
Ram
43k • written 4.0 years ago by
Ankit
▴ 500
0
votes
0
replies
1.8k
views
How to get Gene Co-expression Network from RNA seq data using cor() function?
RNA-Seq
gene-expression-matrix
correlation
R
updated 11 days ago by
Ram
43k • written 6.3 years ago by
aiswaryabioinfo
▴ 30
2
votes
0
replies
1.8k
views
ComBat-seq adjustment of batch effects
RNA-Seq
ComBat-seq
SVA
edgeR
batch-effect
updated 11 days ago by
Ram
43k • written 3.5 years ago by
chatterjee.arumoy
▴ 50
2
votes
2
replies
1.8k
views
Time point microarray data correcting for batch effects
microarray
combat
batch-effect
updated 10 days ago by
Ram
43k • written 6.7 years ago by
tleona3
▴ 10
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat
CNA
Batch-Effect
updated 11 days ago by
Ram
43k • written 5.5 years ago by
sugus
▴ 150
0
votes
5
replies
1.8k
views
Demultiplexing multiple amplicons from one fastq based on primer sequence
demultiplexing
illumina
updated 19 days ago by
Arup Ghosh
3.2k • written 3.4 years ago by
WhiteN8
• 0
1
vote
2
replies
1.8k
views
Data processing order: normalisation or batch effect correction first?
limma
proteome
batch-effect
R
updated 12 days ago by
Ram
43k • written 3.5 years ago by
Sebastian Hesse
▴ 340
0
votes
1
reply
1.8k
views
Advice required for remove batch effect which perfectly collinear with contrast of interest
RNA-seq
batch-effect
updated 10 days ago by
Ram
43k • written 6.6 years ago by
boymin2020
▴ 80
3
votes
5
replies
1.8k
views
Limma/edgeR Design matrix for gender effect
RNA-Seq
batch-effect
updated 12 days ago by
Ram
43k • written 4.7 years ago by
kailsen
• 0
1
vote
0
replies
1.8k
views
Using SVA with RRBS data
sva
batch-effect
RRBS
updated 12 days ago by
Ram
43k • written 7.1 years ago by
mrodrigues.fernanda
▴ 50
1,000 results • Page
4 of 20
Recent Votes
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
A: Hard time trying to calculate Allele Frequency and DP from Platypus
Answer: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
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Comment: NGS forensics: how to know if data is fabricated
by
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8.4k
i've been in our org trying to push such a detector, our use-case is much more limited: I want to make simulated eDNA libraries as real as …
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Comment: NGS forensics: how to know if data is fabricated
by
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3.9k
Can you post an IGV screenshot of what this looks like?
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Yeah some of the Illumina machines pre-trim adapters (not sure if this is still the standard). I've also definitely also seen quality-trimm…
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▴ 540
You can typically find much more useful info in the cif file, for example what you've found is called '_atom_site.pdbx_PDB_ins_code ' and d…
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★ 27k
The best way to find out is to read the original paper. My guess is that the residue has been crystallized in alternative conformations, wh…
Answer: NGS forensics: how to know if data is fabricated
by
Mensur Dlakic
★ 27k
I share the opinion by @philippbayer I have seen enough questionable things in life and in science to keep me permanently jaded, but there…
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
I downloaded the data in two files from the link you provided. With this command: megahit -1 ERR072246_1.fastq.gz -2 ERR072246_2.fastq…
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
If you have Linux the assembly should work on your system, but 8 GB is generally not enough for assembling larger genomes.
Comment: How many reads for WGS Sequencing?
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Mensur Dlakic
★ 27k
I think you might be getting stuck on less relevant parts of my exercise. The most important point was that nothing is wrong with the data.…
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Great comprehensive explanation and overview of the technologies -- with regards to sequencing assays, the one thing I'd add is SNV identif…
Answer: What does it mean single base resolution in sequencing?
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I think that term means slightly different things in different contexts. For example, it's useful to profile mRNA modifications (e.g. m6a) …
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chujie
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Hi, I met the same problem, have you found the solution?
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Hi @fe3e6f65 , In a single sentence, the answer to your question can be summarized as, "*the resolution of a genomic technology refers to …
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