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973 results • Page
2 of 20
Sort: Views
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Views
Votes
Replies
3
votes
2
replies
5.2k
views
RNASeq: Differential gene expression and qqplot
limma
differential-gene-expression
RNA-Seq
deseq2
updated 27 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
2
votes
7
replies
5.2k
views
9 follow
problem with HOMER findMotifsGenome.pl
HOMER
ATAC-Seq
updated 26 days ago by
kaaz
• 0 • written 5.6 years ago by
ste.lu
▴ 80
1
vote
7
replies
5.1k
views
How do I plot several sns.clustermap heatmaps in a single figure?
python
seaborn
updated 26 days ago by
Wubin
▴ 40 • written 3.5 years ago by
roy.granit
▴ 880
0
votes
1
reply
5.0k
views
How to compute a one tail (one way) log rank test for survival?
R
survival
hypothesis-testing
log-rank
updated 26 days ago by
jack
• 0 • written 7.6 years ago by
denalitastic
▴ 30
3
votes
8
replies
5.0k
views
An idea to identify batch effects
microarray
batch-effect
updated 18 days ago by
Ram
43k • written 9.7 years ago by
mjarosz
• 0
23
votes
11
replies
4.9k
views
7 follow
Code golf: detecting homopolymers of length N in the (human) genome
code golf
fasta
homopolymer
repeat
updated 20 days ago by
Ram
43k • written 5.0 years ago by
WouterDeCoster
47k
1
vote
9
replies
4.7k
views
Help with multiple batch effects
sva
combat
batch-effect
updated 20 days ago by
Ram
43k • written 5.9 years ago by
fp89
▴ 30
1
vote
2
replies
4.6k
views
predict TF binding sites from DNA sequence
TF
TRANSFAC
TFBS
binding-site
updated 20 days ago by
Ram
43k • written 6.7 years ago by
grant.hovhannisyan
★ 2.6k
7
votes
3
replies
4.6k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA
RNA-Seq
batch-effect
updated 19 days ago by
Ram
43k • written 5.1 years ago by
tujuchuanli
▴ 100
4
votes
7
replies
4.6k
views
snakemake output directory
snakemake
ngs
updated 20 days ago by
进
• 0 • written 3.9 years ago by
Peter Chung
▴ 200
2
votes
4
replies
4.5k
views
Differential Expression Analysis with monocle and batch effect correction
single-cell
RNA-Seq
batch-effect
updated 19 days ago by
Ram
43k • written 6.0 years ago by
Poorya Parvizi
▴ 60
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq
batch-effect
updated 20 days ago by
Ram
43k • written 7.4 years ago by
denalitastic
▴ 30
12
votes
13
replies
4.4k
views
RNA-Seq DGE using PCA components as covariate
differential-gene-expression
RNA-Seq
glm
DESeq2
updated 27 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
18
votes
20
replies
4.4k
views
6 follow
How to identify significant differentially expressed genes and gene regulatory networks from microarray data.
microarray
differential-gene-expression
updated 27 days ago by
Ram
43k • written 7.6 years ago by
morteza.mahmoudisaber
▴ 80
6
votes
6
replies
4.4k
views
10x to cloupe
single-cell-transcriptomics
10x
27 days ago by
firestar
★ 1.6k
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 27 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 270
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression
RNA-seq
updated 27 days ago by
Ram
43k • written 6.2 years ago by
pablo61991
▴ 90
3
votes
2
replies
4.2k
views
Batch effects in sequencing data
batch-effect
updated 18 days ago by
Ram
43k • written 8.7 years ago by
Andrew
▴ 60
3
votes
8
replies
4.2k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm
scRNA-seq
RNA-Seq
tpm
batch-effect
updated 18 days ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq
deseq2
batch-effect
updated 19 days ago by
Ram
43k • written 5.0 years ago by
Mozart
▴ 330
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 18 days ago by
Ram
43k • written 7.7 years ago by
Lluís R.
★ 1.2k
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression
Salmon
updated 27 days ago by
Ram
43k • written 5.6 years ago by
lkianmehr
▴ 100
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray
r
GEOquery
updated 20 days ago by
Ram
43k • written 5.0 years ago by
mosesoo
▴ 30
1
vote
10
replies
4.0k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 22 days ago by
Aspire
▴ 330 • written 19 months ago by
Manav
• 0
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq
batch-effect
updated 19 days ago by
Ram
43k • written 4.8 years ago by
Rimma
▴ 30
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 6 days ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
3
votes
4
replies
3.9k
views
Error in ComBat function: Error in dat[, batch == batch_level] : (subscript) logical subscript too long
Batch-effect
microarray
R
updated 20 days ago by
Ram
43k • written 2.9 years ago by
Sib
▴ 60
30
votes
12
replies
3.8k
views
Trying to understand the maths behind one Limma function
limma
RNA-Seq
batch-effect
updated 21 days ago by
Ram
43k • written 4.0 years ago by
Mozart
▴ 330
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 17 hours ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq
batch-effect
DESeq2
Salmon
updated 18 days ago by
Ram
43k • written 6.5 years ago by
georgewwp
▴ 30
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 13 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
2
votes
6
replies
3.7k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 11 days ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
2
votes
6
replies
3.7k
views
Algorithm to remove batch effects
single-cell
batch-effect
RNA-Seq
updated 20 days ago by
Ram
43k • written 3.3 years ago by
fouerghi20
▴ 80
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 27 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt
getBM
R
updated 20 days ago by
Ram
43k • written 5.2 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 18 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 12 days ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
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 18 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
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 19 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 20 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq
countOverlaps
R
updated 20 days ago by
Ram
43k • written 6.3 years ago by
seta
★ 1.9k
1
vote
3
replies
3.4k
views
How to correct for batch effect in microarray meta-analysis
ComBat
microarray
meta-analysis
batch-effect
updated 18 days ago by
Ram
43k • written 10.0 years ago by
BrunoGiotti
▴ 120
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 20 days ago by
Ram
43k • written 5.3 years ago by
Davide Chicco
▴ 120
3
votes
4
replies
3.3k
views
Motif analysis of DMRs (Differentially Methylated Regions) by HOMER
next-gen
updated 25 days ago by
Ram
43k • written 6.7 years ago by
inschigu
▴ 10
1
vote
3
replies
3.3k
views
How to calculate Differential Gene expression between samples with replicates
Differential-Gene-Expression
RNA-Seq
updated 27 days ago by
Ram
43k • written 7.9 years ago by
doncheng1
• 0
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat
R
SVA
Biostatistics
batch-effect
updated 18 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 20 days ago by
Ram
43k • written 8.5 years ago by
AB
▴ 360
1
vote
4
replies
3.2k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 18 days ago by
Ram
43k • written 7.1 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 19 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 18 days ago by
Ram
43k • written 9.0 years ago by
siddharth.patel.153
• 0
973 results • Page
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Recent Votes
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Comment: Which hg38 file?
Answer: Which hg38 file?
Answer: Where to get the following bed file?
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Comment: How to compute TPM normalized values for TCGA miRNA data?
by
swbarnes2
14k
When everything is the same size, correcting for size is pointless. It doesn't change the numbers much at all.
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What do the alignments look like in IGV?
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I solved the problem! Thanks!
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Thank you, here I am giving you some example , suppose I have bam files . 1.bam 2.bam 3.bam 4.bam now I want to see Spike gene coverage in …
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I would like to download top markers for each subpopulation data. Is there no way? It seems different from the DGE data.
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Refer to SAM alignment format: https://samtools.github.io/hts-specs/SAMv1.pdf Check section 1.4.
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Step 1: Go to TCGA in the GDC and open the Cohort Builder https://portal.gdc.cancer.gov/analysis_page?app=CohortBuilder&tab=general Step …
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142k
SeqCap kits are discontinued. If you don't find the said file your will need to email Roche Support per this page: https://sequencing.roche…
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3.9k
UCSC maintains a list of exome probe sets and targets. You could check there: https://hgdownload.soe.ucsc.edu/gbdb/hg19/exomeProbesets/
Comment: How to compute TPM normalized values for TCGA miRNA data?
by
Ngrin
• 0
Yes, I found some similar ideas on biostar repository. So you think the authors have done something wrong? And I should only consider CPM?
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It is difficult to answer how they were able to identify *S. hominis* without seeing the code or paper. To address your second question, i…
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Did you check where the `features.tsv.gz` file had Gene IDs or Ensembl IDs?
Answer: How to compute TPM normalized values for TCGA miRNA data?
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TPM is irrelevant for miRNA-seq; CPM works fine. TPM tries to adjust for length effects by dividing by gene length (e.g. reducing the im…
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