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1,000 results • Page
5 of 20
Sort: Views
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Views
Votes
Replies
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat
CNA
Batch-Effect
updated 8 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 17 days ago by
Arup Ghosh
3.2k • written 3.4 years ago by
WhiteN8
• 0
3
votes
5
replies
1.8k
views
Limma/edgeR Design matrix for gender effect
RNA-Seq
batch-effect
updated 9 days ago by
Ram
43k • written 4.7 years ago by
kailsen
• 0
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 7 days ago by
Ram
43k • written 6.6 years ago by
boymin2020
▴ 80
2
votes
5
replies
1.8k
views
6 follow
DNA methylation preprocessing
Funnorm
methylation
Raw
SWAN
DNA
updated 25 days ago by
sup0903
• 0 • written 2.3 years ago by
SYOSY
▴ 10
1
vote
2
replies
1.8k
views
Data processing order: normalisation or batch effect correction first?
limma
proteome
batch-effect
R
updated 9 days ago by
Ram
43k • written 3.5 years ago by
Sebastian Hesse
▴ 340
1
vote
0
replies
1.8k
views
Using SVA with RRBS data
sva
batch-effect
RRBS
updated 9 days ago by
Ram
43k • written 7.1 years ago by
mrodrigues.fernanda
▴ 50
0
votes
4
replies
1.8k
views
Correcting batch effect in unevenly distributed groups
RNA-Seq
batch-effect
R
updated 8 days ago by
Ram
43k • written 4.8 years ago by
jperezboza
▴ 20
2
votes
2
replies
1.8k
views
EdgeR in Galaxy. Adjust C-value?
Differential-gene-expression
EdgeR
Galaxy
C-value
updated 16 days ago by
Ram
43k • written 7.6 years ago by
ando.kelli
▴ 60
0
votes
0
replies
1.8k
views
Differential expression using Scran batch corrected data
single-cell
Batch-effect
RNA-Seq
Scran
updated 7 days ago by
Ram
43k • written 5.5 years ago by
baldissera152
▴ 10
4
votes
2
replies
1.8k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 9 days ago by
Dr.Animo
▴ 130 • written 12 months ago by
BioinfoBee
• 0
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 9 days ago by
Ram
43k • written 2.9 years ago by
Mat
▴ 60
0
votes
0
replies
1.7k
views
Accounting for hidden batch effects in differential expression analysis with DEXseq and Slueth
Batch-effect
RNA-Seq
Differential-Expression
updated 9 days ago by
Ram
43k • written 7.2 years ago by
vakul.mohanty
▴ 270
1
vote
3
replies
1.7k
views
Using Nanoplot to asses quality of ONT data
ONT
Long-read-sequencing
NanoPlot
updated 20 days ago by
Ram
43k • written 2.3 years ago by
matt81rd
▴ 10
1
vote
2
replies
1.7k
views
Batch effects and MDSPlot in limma
limma
Batch-effect
MDS
Galaxy
updated 9 days ago by
Ram
43k • written 4.8 years ago by
sonayuv
• 0
1
vote
1
reply
1.7k
views
sea corrected expression matrix
sva
microarrays
batch-effect
updated 9 days ago by
Ram
43k • written 6.8 years ago by
ATCG
▴ 380
2
votes
2
replies
1.7k
views
Remove batch effect for many RNA-seq
ComBat
RNA-Seq
batch-effect
sva
updated 8 days ago by
Ram
43k • written 4.8 years ago by
Shaway
• 0
1
vote
4
replies
1.7k
views
Batch correction and DE analysis of miRNA Seq data
miRNAseq
Differential-Expression
batch-effect
updated 7 days ago by
Ram
43k • written 5.1 years ago by
georgians
▴ 50
0
votes
0
replies
1.7k
views
Differential Gene Expression Analysis using two distinct scRNA-seq datasets
differential-gene-expression
RNA-Seq
scRNA-seq
updated 16 days ago by
Ram
43k • written 6.5 years ago by
Eskimo
▴ 120
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 8 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
0
votes
0
replies
1.7k
views
Batch effect and CCA
CCA
RNA-Seq
seurat
batch-effect
updated 8 days ago by
Ram
43k • written 5.1 years ago by
akivab2
▴ 110
2
votes
2
replies
1.6k
views
How to add a title to a cnetplot?
r
cnetplot
updated 9 days ago by
Ram
43k • written 3.5 years ago by
appropiate
▴ 80
0
votes
5
replies
1.6k
views
what does mean this error ? "(ERR): hisat2-align exited with value 1" in mapping long noncoding RNAs
long-non-coding-RNA
lncRNA
updated 20 days ago by
Ram
43k • written 2.6 years ago by
reza
• 0
0
votes
1
reply
1.6k
views
RRBS data analysis using RnBeads give Scan() error
RRBS
450k
RnBeads
updated 9 days ago by
Ram
43k • written 6.7 years ago by
rahel14350
▴ 40
2
votes
2
replies
1.6k
views
Combining control samples from 2 separate studies. Model matrix for batch effect?
gene-expression
R
limma
batch-effect
model-matrix
updated 7 days ago by
Ram
43k • written 7.2 years ago by
tolgaturant
▴ 20
0
votes
1
reply
1.6k
views
Public RNA-Seq and Microarray samples from same tissue
Microarray
RNA-Seq
Batch-Effect
updated 9 days ago by
Ram
43k • written 7.9 years ago by
Ar
★ 1.1k
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads
RNA-seq
gene-expression
read-count
updated 20 days ago by
Ram
43k • written 2.9 years ago by
gat
• 0
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma
sva
batch-effect
R
updated 10 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
24 days ago by
b.contreras.moreira
▴ 170
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat
RNA-Seq
Limma
DESeq2
batch-effect
updated 7 days ago by
Ram
43k • written 4.9 years ago by
borkk
▴ 140
0
votes
1
reply
1.6k
views
Extraction of batch subject sequence from Blast result.
minus-strand
blastdbcmd
updated 9 days ago by
Ram
43k • written 5.9 years ago by
kabir.deb
▴ 80
2
votes
5
replies
1.6k
views
Adding functional annotation and meta-data of MAKER/BRAKER GFF
metadata
functional-annotation
BRAKER
MAKER
updated 24 days ago by
andorjkiss
▴ 40 • written 15 months ago by
javanokendo
▴ 60
5
votes
12
replies
1.5k
views
Subbmission Data
RNA-seq
updated 23 days ago by
Ram
43k • written 14 months ago by
GiV17
▴ 50
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq
edgeR
DESeq2
Batch-Effect
updated 9 days ago by
Ram
43k • written 5.2 years ago by
Behram Radmanesh
▴ 40
4
votes
10
replies
1.5k
views
Do I have batch effect?
RNA-Seq
edgeR
batch-effect
updated 10 days ago by
Ram
43k • written 3.9 years ago by
avino
▴ 20
3
votes
6
replies
1.5k
views
edgeR FDR always 1
FDR
differential-gene-expression
edgeR
miRNA
updated 16 days ago by
Ram
43k • written 4.9 years ago by
AngAdd
▴ 20
2
votes
3
replies
1.5k
views
Duplicate row name not allowed while reading the file in R
RNA-Seq
deseq2
Differential-Gene-expression
R
updated 16 days ago by
Ram
43k • written 4.9 years ago by
imanbh
• 0
1
vote
5
replies
1.5k
views
How to correct unknown Batch effect?
PCA
gene-expression
DESeq2
RNA-seq
batch-effect
updated 9 days ago by
Ram
43k • written 12 months ago by
luffy
▴ 110
9
votes
6
replies
1.5k
views
What in silico PCR commandline tool do you use that can handle IUPAC characters?
pcr
amplicon
primer
updated 23 days ago by
Ram
43k • written 16 months ago by
O.rka
▴ 710
0
votes
0
replies
1.5k
views
RIPSeeker viewRIP function fails to extract values() in GRangesList/S4 object
RIPSeq
S4
RIP
R
updated 9 days ago by
Ram
43k • written 6.2 years ago by
CrisMar
▴ 80
0
votes
0
replies
1.5k
views
minifi for RRBS
rrbs
batch-effect
methylation
updated 9 days ago by
Ram
43k • written 7.1 years ago by
German.M.Demidov
★ 2.9k
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq
quantification
alignment
updated 9 days ago by
Ram
43k • written 5.1 years ago by
mohammedtoufiq91
▴ 250
2
votes
3
replies
1.5k
views
RNASeq - How to compare the expression of a single gene across batches
RNA-Seq
edgeR
batch-effect
updated 7 days ago by
Ram
43k • written 3.5 years ago by
oakhamwolf
▴ 20
1
vote
5
replies
1.5k
views
Blastn in galaxy
Blastn
galaxy
updated 23 days ago by
Ram
43k • written 3.0 years ago by
adnan.lahuf
• 0
0
votes
1
reply
1.4k
views
Assembled genome a little larger than Kmergeneie prediction?
kmergenie
genome-size
updated 9 days ago by
Ram
43k • written 8.0 years ago by
gerrychang1985
▴ 40
4
votes
6
replies
1.4k
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3
GenomicRanges
ORFik
GenomicFeatures
updated 11 days ago by
GenoMax
141k • written 15 months ago by
Estefania
▴ 30
0
votes
0
replies
1.4k
views
Help with Circos plot "Assumption Error" that prevents plotting a protein interactions network
CircosPlot
updated 9 days ago by
Ram
43k • written 3.3 years ago by
hniels01
• 0
1
vote
2
replies
1.4k
views
gdc-client command line error
line
GDC
TCGA
command
updated 22 days ago by
Yuju
• 0 • written 20 months ago by
apronstring
• 0
10
votes
5
replies
1.4k
views
6 follow
Courses in RNAseq data
RNA-seq
Courses
updated 23 days ago by
Ram
43k • written 2.5 years ago by
margot.27.muller
▴ 30
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray
combat
batch-effect
median-normalization
updated 7 days ago by
Ram
43k • written 18 months ago by
Dominique
• 0
1,000 results • Page
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Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
by
bk11
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
by
GenoMax
141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely mapping in regions whe…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq
by
pinheirofabiano
▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question
by
starswillfade
▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question
by
starswillfade
▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Comment: genome assembly records not present in assembly_summary.txt
by
GenoMax
141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
Comment: what is the purpose of indexing the reference genome (Kallisto)
by
i.sudbery
19k
Specifically: If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
benformatics
3.9k
This is way easier to do solely in R now 10 years later. library(GenomicFeatures) library(rtracklayer) ## import GTF…
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