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372 results • Page
5 of 8
Sort: replies
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Replies
0
votes
2
replies
235
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
6 days ago by
mropri
▴ 150
0
votes
2
replies
1.2k
views
Normalization (microarray data)
microarray
Normalization
Batch-effect
updated 4 days ago by
Ram
43k • written 6.3 years ago by
j_jamal96
▴ 20
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq
batch-effect
DESeq2
Salmon
updated 4 days ago by
Ram
43k • written 6.5 years ago by
georgewwp
▴ 30
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 4 days ago by
Ram
43k • written 6.5 years ago by
Alternative
▴ 270
0
votes
2
replies
299
views
GSEA analysis in R
GSEA
R
Arabidopsis
5 days ago by
Sudip
• 0
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 6 days ago by
Dr.Animo
▴ 130 • written 12 months ago by
BioinfoBee
• 0
2
votes
2
replies
1.8k
views
Time point microarray data correcting for batch effects
microarray
combat
batch-effect
updated 4 days ago by
Ram
43k • written 6.7 years ago by
tleona3
▴ 10
1
vote
2
replies
2.9k
views
Taking surrogate variable into account before running PCA
sva
svaseq
batch-effect
updated 4 days ago by
Ram
43k • written 6.9 years ago by
wamiqsaifi
• 0
0
votes
2
replies
111
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
15 hours ago by
dxj294
• 0
0
votes
2
replies
126
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 17 hours ago by
Mensur Dlakic
★ 27k • written 23 hours ago by
emmanouil.a
▴ 120
0
votes
2
replies
124
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
15 hours ago by
sainavyav22
• 0
2
votes
2
replies
1.6k
views
How to add a title to a cnetplot?
r
cnetplot
updated 6 days ago by
Ram
43k • written 3.5 years ago by
appropiate
▴ 80
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 4 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
3
votes
2
replies
2.1k
views
Batch effect correction - miRNA sequencing - DESeq2
Batch-effect
DESeq2
miRNA-Seq
updated 6 days ago by
Ram
43k • written 5.5 years ago by
prekrish
• 0
0
votes
2
replies
151
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 18 hours ago by
i.sudbery
19k • written 21 hours ago by
Patadu94
• 0
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 4 days ago by
Ram
43k • written 7.2 years ago by
tolgaturant
▴ 20
4
votes
2
replies
268
views
Forum:
Bioinformatics: Where do I start
Sequencing
updated 6 days ago by
Ram
43k • written 7 days ago by
Adi
▴ 10
3
votes
2
replies
239
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
22 hours ago by
kristiewyleung
• 0
3
votes
2
replies
1.0k
views
Can I take 'organ type' as a batch effect and use ComBat to remove organ dependent variations?
RNA-Seq
Cross-Species
SVA
ComBat
Batch-Effect
updated 6 days ago by
Ram
43k • written 4.6 years ago by
rodguinea
• 0
1
vote
2
replies
1.4k
views
How to download a list pdb codes contained in a csv file using
Biopython
updated 6 days ago by
Ram
43k • written 3.1 years ago by
jmungar2
▴ 10
0
votes
2
replies
163
views
Result of running of p3_in.pl
primer3
updated 1 day ago by
GenoMax
141k • written 1 day ago by
nasri
• 0
0
votes
2
replies
279
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
6 days ago by
Koketso
• 0
3
votes
2
replies
4.1k
views
Batch effects in sequencing data
batch-effect
updated 4 days ago by
Ram
43k • written 8.7 years ago by
Andrew
▴ 60
2
votes
2
replies
379
views
I am new to single cell analysis. Can RNA velocity (spliced/unspliced) be calculated solely from the raw file (count matrix) provided in the Suppleme…
GEO
velocity
count-matrix
updated 6 days ago by
Ram
43k • written 7 days ago by
Spring
• 0
0
votes
2
replies
46
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 40 minutes ago by
GenoMax
141k • written 2 hours ago by
rhossen
• 0
1
vote
2
replies
221
views
permutation test in edgeR
rna-seq
edgeR
updated 1 day ago by
Gordon Smyth
★ 7.0k • written 15 days ago by
Netanel
• 0
2
votes
2
replies
234
views
How to filter columns in a raw sparse matrix in R
matrix
R
updated 6 days ago by
bk11
★ 2.3k • written 6 days ago by
bgbs
• 0
4
votes
2
replies
306
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 5 days ago by
Juke34
8.5k • written 5 days ago by
njornet
▴ 20
1
vote
1
reply
2.8k
views
removing batch effects from large number of data sets
Microarray
batch-effect
updated 6 days ago by
Ram
43k • written 5.9 years ago by
nazaninhoseinkhan
▴ 520
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 5 days ago by
Ram
43k • written 5.5 years ago by
Poorya Parvizi
▴ 60
0
votes
1
reply
1.6k
views
RRBS data analysis using RnBeads give Scan() error
RRBS
450k
RnBeads
updated 6 days ago by
Ram
43k • written 6.7 years ago by
rahel14350
▴ 40
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect
R
updated 5 days ago by
Ram
43k • written 6.1 years ago by
Jun
• 0
1
vote
1
reply
265
views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf
bam
bcf
snps
updated 5 days ago by
LChart
3.9k • written 5 days ago by
George
▴ 10
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 5 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
1
reply
259
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 5 days ago by
GenoMax
141k • written 5 days ago by
ycts
• 0
3
votes
1
reply
593
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 5 days ago by
etiennedanis
▴ 20 • written 19 months ago by
DareDevil
★ 4.3k
2
votes
1
reply
248
views
Pediococcus acidilactici sequence analysis
BLAST
Gene-Ontology
updated 5 days ago by
Ram
43k • written 5 days ago by
anasjamshed
▴ 120
0
votes
1
reply
3.1k
views
Removing batch effects from RPKM data
limma
removeBatchEffect
batch-effect
rpkm
updated 6 days ago by
Ram
43k • written 8.5 years ago by
AB
▴ 360
0
votes
1
reply
260
views
10x VDJ (TCR/BCR) BAM to fastq
TCR
VDJ
BCR
10x
updated 5 days ago by
GenoMax
141k • written 5 days ago by
predeus
★ 1.9k
0
votes
1
reply
93
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 16 hours ago by
Ram
43k • written 16 hours ago by
Cameron.walker9900
• 0
0
votes
1
reply
396
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 4 days ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
1
reply
259
views
DEseq2
RNA-seq
DESeq2
updated 4 days ago by
Ram
43k • written 5 days ago by
rrehimi
• 0
1
vote
1
reply
1.7k
views
sea corrected expression matrix
sva
microarrays
batch-effect
updated 6 days ago by
Ram
43k • written 6.8 years ago by
ATCG
▴ 380
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 4 days ago by
Ram
43k • written 4.8 years ago by
BioLite
▴ 20
0
votes
1
reply
1.2k
views
Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
random-effects
RNA-Seq
batch-effect
updated 6 days ago by
Ram
43k • written 6.8 years ago by
Dipro
• 0
1
vote
1
reply
360
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
4 days ago by
otieno43
▴ 30
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 6 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
1
reply
2.9k
views
Microarray batch effect correction
Microarray
Batch-effect
updated 4 days ago by
Ram
43k • written 6.6 years ago by
sarahmanderni
▴ 100
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 4 days ago by
Ram
43k • written 6.6 years ago by
boymin2020
▴ 80
1
vote
1
reply
656
views
Save experiment with batch effects - Protein microarray
statistics
protein-array
batch-effect
updated 6 days ago by
Ram
43k • written 4.4 years ago by
s.lima.diogenes
▴ 10
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