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750 results • Page
2 of 15
Sort: Views
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Views
Votes
Replies
1
vote
4
replies
3.2k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 29 days ago by
Ram
43k • written 7.2 years ago by
hellocita
▴ 40
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 29 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 29 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 29 days ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
7
votes
3
replies
3.0k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 29 days ago by
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
2
votes
14
replies
3.0k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 3 days ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
1
vote
2
replies
3.0k
views
Taking surrogate variable into account before running PCA
sva
svaseq
batch-effect
updated 29 days ago by
Ram
43k • written 6.9 years ago by
wamiqsaifi
• 0
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 3 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
4
votes
3
replies
2.9k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq
picard
validatesamfile
updated 8 days ago by
Pierre Lindenbaum
161k • written 9 days ago by
Lila M
★ 1.2k
0
votes
1
reply
2.9k
views
Microarray batch effect correction
Microarray
Batch-effect
updated 29 days ago by
Ram
43k • written 6.7 years ago by
sarahmanderni
▴ 100
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 18 days ago by
dimpleadiwal050896
• 0 • written 5.0 years ago by
ggman
▴ 90
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 29 days ago by
Ram
43k • written 7.1 years ago by
endikavarela
• 0
2
votes
4
replies
2.7k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel
gatk
calling
snp
variant
updated 18 days ago by
Medhat
9.7k • written 2.0 years ago by
Vitor1
▴ 120
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 23 days ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
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
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 29 days ago by
Ram
43k • written 9.2 years ago by
chengzhao41
▴ 110
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 13 days ago by
Ruqaiya
• 0 • written 10.2 years ago by
Yuelin
▴ 20
0
votes
9
replies
2.6k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 19 days ago by
Ram
43k • written 9 months ago by
Gio
• 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 29 days ago by
Ram
43k • written 7.1 years ago by
alexis.vandenbon
▴ 80
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS
insertion site
trangene
de-novo
soap
updated 9 days ago by
Cameron.walker9900
• 0 • written 5.1 years ago by
Assa Yeroslaviz
★ 1.8k
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 25 days ago by
chrchang523
10k • written 6.2 years ago by
Ginevra
▴ 10
1
vote
14
replies
2.5k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 15 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
2
votes
4
replies
2.5k
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 23 days ago by
ZhangYuanfeng
• 0 • written 2.5 years ago by
Frazier Baker
• 0
3
votes
3
replies
2.4k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 22 days ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 5 days ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
2
votes
1
reply
2.3k
views
TCGA RNAseqV2 data matrix batch effect control and remove
RNA-Seq
batch-effect
updated 29 days ago by
Ram
43k • written 7.7 years ago by
fractal61
▴ 10
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 3 days ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
38
votes
24
replies
2.3k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 18 days ago by
i.sudbery
19k • written 20 days ago by
noodle
▴ 580
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing
bowtie2
alignment
samtools
ngs
updated 14 days ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 29 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 29 days ago by
Ram
43k • written 6.9 years ago by
Ar
★ 1.1k
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 8 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
18 days ago by
anna
▴ 20
1
vote
3
replies
2.0k
views
gene expression data analysis and batch effect methods
microarray
Gene-expression
batch-effect
updated 29 days ago by
Ram
43k • written 7.0 years ago by
Shamim Sarhadi
▴ 220
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 21 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
0
votes
0
replies
2.0k
views
NOISeq Batch Correction to RNA-seq data
Batch-effect
RNA-Seq
ARSyNseq
limma
NOISeq
updated 29 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
5
votes
13
replies
2.0k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 27 days ago by
ATpoint
82k • written 28 days ago by
BioinfGuru
★ 1.7k
0
votes
0
replies
2.0k
views
Correcting batch effect from known variables in RnBeads using Combat
Combat
450k
methylation
RnBeads
batch-effect
updated 29 days ago by
Ram
43k • written 7.2 years ago by
rahel14350
▴ 40
0
votes
0
replies
2.0k
views
batch effect in radseq
radseq
batch-effect
SNP
updated 29 days ago by
Ram
43k • written 7.5 years ago by
oselm
▴ 50
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 2 days ago by
Ram
43k • written 3.9 years ago by
millere
• 0
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 29 days ago by
Ram
43k • written 6.6 years ago by
Alternative
▴ 290
0
votes
7
replies
1.9k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering
dendrogram
RNA-Seq
batch-effect
updated 29 days ago by
Ram
43k • written 4.1 years ago by
Ankit
▴ 500
2
votes
2
replies
1.8k
views
Time point microarray data correcting for batch effects
microarray
combat
batch-effect
updated 29 days ago by
Ram
43k • written 6.7 years ago by
tleona3
▴ 10
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
updated 12 days ago by
MiladAD
▴ 10 • written 2.0 years ago by
soheil
• 0
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 14 days ago by
e.r.zakiev
▴ 210 • written 3.9 years ago by
n.anuragsharma
▴ 40
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 29 days ago by
Ram
43k • written 6.7 years ago by
boymin2020
▴ 80
0
votes
0
replies
1.8k
views
Differential expression using Scran batch corrected data
single-cell
Batch-effect
RNA-Seq
Scran
updated 29 days ago by
Ram
43k • written 5.5 years ago by
baldissera152
▴ 10
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
3 days ago by
Arton
▴ 10
1
vote
4
replies
1.7k
views
Batch correction and DE analysis of miRNA Seq data
miRNAseq
Differential-Expression
batch-effect
updated 29 days ago by
Ram
43k • written 5.1 years ago by
georgians
▴ 50
1
vote
2
replies
1.7k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 9 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
750 results • Page
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Recent Replies
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Our resul…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
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Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
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by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
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hophuquy0944
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i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
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Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot
by
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4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot
by
bk11
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You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
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ntsopoul
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I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
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There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
bk11
★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
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