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827 results • Page
2 of 17
Sort: Views
Rank
Views
Votes
Replies
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq
batch-effect
DESeq2
Salmon
updated 28 days ago by
Ram
43k • written 6.6 years ago by
georgewwp
▴ 30
25
votes
11
replies
3.8k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 23 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
2
votes
6
replies
3.8k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 21 days ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt
getBM
R
updated 29 days ago by
Ram
43k • written 5.3 years ago by
Corentin
▴ 600
1
vote
3
replies
3.6k
views
Does Harmony batch correction for scRNA-seq require the same populations to be present in all samples?
Harmony
single-cell
scRNA-seq
batch-effect
updated 28 days ago by
Ram
43k • written 4.6 years ago by
Lucy
▴ 140
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 22 days ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 3 days ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
1
vote
8
replies
3.5k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 29 days ago by
Ram
43k • written 7.1 years ago by
tud55122
▴ 20
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 28 days ago by
Ram
43k • written 7.2 years ago by
dyollluap
▴ 310
2
votes
10
replies
3.5k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 29 days ago by
Ram
43k • written 7.5 years ago by
linda
• 0
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq
countOverlaps
R
updated 29 days ago by
Ram
43k • written 6.4 years ago by
seta
★ 1.9k
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 8 days ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 60
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 29 days ago by
Ram
43k • written 5.3 years ago by
Davide Chicco
▴ 120
1
vote
3
replies
3.4k
views
How to correct for batch effect in microarray meta-analysis
ComBat
microarray
meta-analysis
batch-effect
updated 28 days ago by
Ram
43k • written 10.0 years ago by
BrunoGiotti
▴ 120
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat
R
SVA
Biostatistics
batch-effect
updated 28 days ago by
Ram
43k • written 7.5 years ago by
mkhadka10
• 0
0
votes
1
reply
3.2k
views
Removing batch effects from RPKM data
limma
removeBatchEffect
batch-effect
rpkm
updated 29 days ago by
Ram
43k • written 8.6 years ago by
AB
▴ 360
1
vote
4
replies
3.2k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 28 days ago by
Ram
43k • written 7.2 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 29 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 28 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 28 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
0
votes
2
replies
3.0k
views
Should I pre-normalize RNAseq data before combat?
RNA-Seq
combat
batch-effect
R
updated 29 days ago by
Ram
43k • written 4.8 years ago by
zhaoliang0302
▴ 50
7
votes
3
replies
3.0k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 27 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 28 days ago by
Ram
43k • written 6.9 years ago by
wamiqsaifi
• 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 2 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 2 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 7 days ago by
Pierre Lindenbaum
161k • written 7 days ago by
Lila M
★ 1.2k
0
votes
1
reply
2.9k
views
Microarray batch effect correction
Microarray
Batch-effect
updated 28 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 17 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 28 days ago by
Ram
43k • written 7.1 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 29 days ago by
Ram
43k • written 5.2 years ago by
grant.hovhannisyan
★ 2.6k
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 17 days ago by
Medhat
9.7k • written 2.0 years ago by
Vitor1
▴ 120
0
votes
0
replies
2.7k
views
Comparing lists generated by Counter() and .most_common() for AA seqs
python
amino-acid
updated 29 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
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 28 days ago by
Ram
43k • written 9.2 years ago by
chengzhao41
▴ 110
4
votes
4
replies
2.6k
views
Advice on Handling Batch Effect in ChIP-seq Experiment
ChIP-Seq
batch-effect
sequencing
updated 29 days ago by
Ram
43k • written 4.7 years ago by
dmj6ab
▴ 20
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 12 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 17 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 28 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 8 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
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 21 days ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
1
vote
14
replies
2.4k
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
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect
omniexpress
GWAS
GSA
updated 29 days ago by
Ram
43k • written 4.9 years ago by
saksis.rihards
▴ 10
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 4 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 28 days ago by
Ram
43k • written 7.7 years ago by
fractal61
▴ 10
827 results • Page
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Hello It appears that the file path or file permissions may be the cause of the problem. Verify that the file "/geneInfo.tab" is present…
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You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
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What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
Comment: Merge clusters in Seurat UMAP
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Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP
by
bk11
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I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
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Gabriel R.
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I know about it, isn't there a simple C++ static binary?
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Gabriel R.
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needle is great! but it does not handle sequences of 100k or so.
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Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
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The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
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Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
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