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762 results • Page
2 of 16
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 28 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 28 days ago by
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
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
2
votes
14
replies
2.9k
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
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 8 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
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 29 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 22 days ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 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
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
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 29 days ago by
John Marshall
3.0k • written 2.0 years ago by
bioguy24
▴ 230
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 18 days ago by
Ram
43k • written 8 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 24 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 14 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
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 22 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 2 days ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
38
votes
24
replies
2.2k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 17 days ago by
i.sudbery
19k • written 19 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
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
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
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 20 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
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
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 1 day ago by
Ram
43k • written 3.9 years ago by
millere
• 0
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
2 days ago by
Arton
▴ 10
762 results • Page
2 of 16
Recent Votes
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Differentially Expressed Genes between two conditions (scRNA, single GEO dataset with multiple samples and no cell annotations)
Differentially expressed genes between Seurat objects
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Recent Replies
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.
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
Comment: how to treat the replicates while performing WGCNA
by
andres.firrincieli
3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
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For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
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Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs
by
BATMAN
• 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thank you. What exactly do you mean? Changing `ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_cluster…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Try tweaking the `gp` of the rowAnnotation instead of tweaking the `annotation_name_gp` - that might do the trick.
Comment: Help! Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
Comment: Details on salmon index
by
Rob
6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
Comment: Help! Reconstruction of locus, order contigs
by
BATMAN
• 0
Thanks for your reply, my idea is not to have to write it down. What I have is an alignment of the .gbk from the progressiveMauve. It would…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
I did some digging aroumd, no static binary. Plus it seems you need to roll your own program.
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
We tested it, however, it does not seem to produce a fast a file of the results or anything that we can easily parse. It produces a CIGAR a…
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