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1,064 results • Page
3 of 22
Sort: Views
Rank
Views
Votes
Replies
3
votes
4
replies
3.3k
views
Motif analysis of DMRs (Differentially Methylated Regions) by HOMER
next-gen
updated 21 days ago by
Ram
43k • written 6.7 years ago by
inschigu
▴ 10
1
vote
3
replies
3.3k
views
How to calculate Differential Gene expression between samples with replicates
Differential-Gene-Expression
RNA-Seq
updated 23 days ago by
Ram
43k • written 7.9 years ago by
doncheng1
• 0
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat
R
SVA
Biostatistics
batch-effect
updated 14 days ago by
Ram
43k • written 7.4 years ago by
mkhadka10
• 0
0
votes
1
reply
3.2k
views
Removing batch effects from RPKM data
limma
removeBatchEffect
batch-effect
rpkm
updated 16 days ago by
Ram
43k • written 8.5 years ago by
AB
▴ 360
1
vote
4
replies
3.1k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 14 days ago by
Ram
43k • written 7.1 years ago by
hellocita
▴ 40
2
votes
1
reply
3.1k
views
Batch effect correction in DE analysis of single cell RNA-seq data and visualization
Seurat
Batch-effect
SCDE
RNA-Seq
Limma
updated 15 days ago by
Ram
43k • written 5.5 years ago by
Poorya Parvizi
▴ 60
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 14 days ago by
Ram
43k • written 9.0 years ago by
siddharth.patel.153
• 0
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 14 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression
RNA-seq
updated 23 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 14 days ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
0
votes
2
replies
3.0k
views
Should I pre-normalize RNAseq data before combat?
RNA-Seq
combat
batch-effect
R
updated 15 days ago by
Ram
43k • written 4.8 years ago by
zhaoliang0302
▴ 50
1
vote
2
replies
2.9k
views
Taking surrogate variable into account before running PCA
sva
svaseq
batch-effect
updated 14 days ago by
Ram
43k • written 6.9 years ago by
wamiqsaifi
• 0
0
votes
1
reply
2.9k
views
Microarray batch effect correction
Microarray
Batch-effect
updated 14 days ago by
Ram
43k • written 6.7 years ago by
sarahmanderni
▴ 100
7
votes
3
replies
2.9k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 14 days ago by
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
2
votes
5
replies
2.8k
views
Batch effect in Axiom Human Origins Array
affymetrix
array
batch-effect
updated 16 days ago by
Ram
43k • written 7.9 years ago by
Simo
▴ 50
0
votes
0
replies
2.8k
views
TCGA RNAseqVer2 batch effects
TCGA
RNA-Seq
batch-effect
updated 16 days ago by
Ram
43k • written 8.6 years ago by
annadv
• 0
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 16 days ago by
hamarillo
▴ 70 • written 5.7 years ago by
silviajserrano
▴ 50
1
vote
5
replies
2.8k
views
Batch effect identification using PCA
PCA
qRT-PCR
R
targeted-assay
Batch-Effect
updated 17 days ago by
Ram
43k • written 3.9 years ago by
mohammedtoufiq91
▴ 250
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 14 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq
RNA-Seq
batch-effect
DESeq2
updated 15 days ago by
Ram
43k • written 5.1 years ago by
grant.hovhannisyan
★ 2.6k
1
vote
1
reply
2.8k
views
removing batch effects from large number of data sets
Microarray
batch-effect
updated 16 days ago by
Ram
43k • written 5.9 years ago by
nazaninhoseinkhan
▴ 520
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 3 days ago by
dimpleadiwal050896
• 0 • written 4.9 years ago by
ggman
▴ 90
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 15 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
7
votes
10
replies
2.7k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch
batch-effect
DESeq2
rna-seq
updated 16 days ago by
Ram
43k • written 2.0 years ago by
mmitra
▴ 60
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 8 days ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 23 days ago by
Ram
43k • written 6.5 years ago by
vikram
▴ 10
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 16 days ago by
Ram
43k • written 6.3 years ago by
jjrin
▴ 40
2
votes
5
replies
2.7k
views
primer design to discriminate sequences in intron-exon MSA
primer
MSA
intron-exon
updated 27 days ago by
Amruta
• 0 • written 6.6 years ago by
Anand Rao
▴ 630
3
votes
16
replies
2.7k
views
design matrix for dge
limma
differential-gene-expression
r
updated 23 days ago by
Ram
43k • written 7.9 years ago by
1234anjalianjali1234
▴ 50
0
votes
0
replies
2.7k
views
Comparing lists generated by Counter() and .most_common() for AA seqs
python
amino-acid
updated 16 days ago by
Ram
43k • written 9.9 years ago by
st.ph.n
★ 2.7k
4
votes
9
replies
2.7k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by
dvelmeshev
• 0
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression
RNA-Seq
DESeq2
updated 23 days ago by
Ram
43k • written 8.1 years ago by
Chris Gene
▴ 80
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 14 days ago by
Ram
43k • written 9.1 years ago by
chengzhao41
▴ 110
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 15 days ago by
John Marshall
3.0k • written 24 months ago by
bioguy24
▴ 230
4
votes
4
replies
2.6k
views
Advice on Handling Batch Effect in ChIP-seq Experiment
ChIP-Seq
batch-effect
sequencing
updated 15 days ago by
Ram
43k • written 4.6 years ago by
dmj6ab
▴ 20
2
votes
4
replies
2.6k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel
gatk
calling
snp
variant
updated 3 days ago by
Medhat
9.7k • written 24 months ago by
Vitor1
▴ 120
0
votes
0
replies
2.6k
views
Removing batch effects from methylation beta values for molecular subtyping/cluster analysis
clustering
beta-values
batch-effect
methylation
updated 16 days ago by
Ram
43k • written 6.7 years ago by
alecmchiu
• 0
6
votes
0
replies
2.6k
views
Tool:
Immuno-Navigator, a batch-corrected database for gene coexpression in the immune system
gene-co-expression
batch-effect
immunology
updated 14 days ago by
Ram
43k • written 7.0 years ago by
alexis.vandenbon
▴ 80
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 4 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
8
votes
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA
batch-effect
gene-expression
updated 24 days ago by
Ram
43k • written 3.5 years ago by
Gene_MMP8
▴ 240
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 10 days ago by
chrchang523
10k • written 6.2 years ago by
Ginevra
▴ 10
0
votes
1
reply
2.4k
views
Job:
Full Stack Web Developer - Cambridge, UK
JavaScript
Python
Visualisation
written 8.4 years ago by
Richard Smith
▴ 400
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 16 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect
omniexpress
GWAS
GSA
updated 15 days ago by
Ram
43k • written 4.8 years ago by
saksis.rihards
▴ 10
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 8 days ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect
DESeq2
combat_seq
updated 24 days ago by
Ram
43k • written 3.7 years ago by
l.uva
▴ 20
1
vote
5
replies
2.4k
views
Shannon vs Simpson for TCR diversity estimation
TCR
shannon
simpson
updated 21 days ago by
ATpoint
82k • written 5.1 years ago by
CY
▴ 750
3
votes
3
replies
2.4k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 7 days ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
12
votes
4
replies
2.3k
views
long read + salmon? (transcript abundance)
long-read
salmon
updated 27 days ago by
Ram
43k • written 14 months ago by
shinyjj
▴ 50
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma
microarray
differential-gene-expression
updated 23 days ago by
Ram
43k • written 6.1 years ago by
fernardo
▴ 170
1,064 results • Page
3 of 22
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Answer: How many reads for WGS Sequencing?
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Comment: How to Calulate Allele Frequency from a VCF File?
Answer: Introduce SNPs on FASTA
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How to Calulate Allele Frequency from a VCF File?
Answer: allele frequency in VCF
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Can you post your setup, so how many groups and their replication number? I can tell you by experience that you need even more replication …
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The tool is called D**E**Seq2. Anyway, if your factor is `factor(conditions, levels = c("control", "mutant"))` then the first level is the …
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It's been a long time since I did this sort of thing, but I have a vague recollection that the mpileup process was made simpler and/or roll…
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Thank you very much for your answer!
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This is great also for multiline fastas
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This only works for the first line of sequences.
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In case it helps: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units
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Yes, why not? If it works for you like that, bingo!
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Hi. I guess it is solved by now, but as I did not find the answer immediately online, here is the answer I posted on a relevant question: h…
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A late reply, but I just solved exactly the same error upon a request in the team. Please see if it helps in case anyone meets the same err…
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Was the spike-in a commercial product, e.g., from Zymo? Can you provide more information about what cells or DNA was spiked into your samp…
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