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976 results • Page
1 of 20
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76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
13 days ago by
Kevin Blighe
87k
103
votes
42
replies
31k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 29 days ago by
Jeremy Leipzig
22k • written 10.5 years ago by
14134125465346445
★ 3.6k
10
votes
37
replies
12k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato
gene
updated 28 days ago by
aziz.hammou
• 0 • written 8.8 years ago by
kevluv93
▴ 170
10
votes
36
replies
5.9k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA
batch-effect
DESeq2
R
updated 21 days ago by
Ram
43k • written 5.7 years ago by
Kristin Muench
▴ 620
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 6 days ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
38
votes
24
replies
2.0k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 8 days ago by
i.sudbery
19k • written 10 days ago by
noodle
▴ 580
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 20 days ago by
Gordon
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
23
votes
23
replies
9.9k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq
removeBatchEffect
batch-effect
edger
updated 21 days ago by
Ram
43k • written 5.3 years ago by
iraia.munoa
▴ 130
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 29 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 270
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 21 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression
RNA-seq
updated 29 days ago by
Ram
43k • written 6.2 years ago by
pablo61991
▴ 90
7
votes
20
replies
6.5k
views
7 follow
Repeat masked gtf files from ensembl
ensembl
RNA-Seq
genome
updated 27 days ago by
e.r.zakiev
▴ 210 • written 4.3 years ago by
kevin.stachelek
▴ 80
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 29 days ago by
Ram
43k • written 7.6 years ago by
morteza.mahmoudisaber
▴ 80
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 20 days ago by
Ram
43k • written 4.6 years ago by
Bogdan
★ 1.4k
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter
visualization
R
updated 21 days ago by
Ram
43k • written 9.6 years ago by
james.lloyd
▴ 100
7
votes
16
replies
765
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
9 days ago by
Ruqaiya
• 0
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 19 days ago by
Hagen
▴ 10 • written 10.2 years ago by
filipzembol
▴ 180
3
votes
16
replies
2.7k
views
design matrix for dge
limma
differential-gene-expression
r
updated 29 days ago by
Ram
43k • written 7.9 years ago by
1234anjalianjali1234
▴ 50
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 1 day ago by
Pierre Lindenbaum
161k • written 5.7 years ago by
mostafarafiepour
▴ 180
0
votes
16
replies
1.1k
views
What is the sequence origin in human plasma?
human
sequence
cfDNA
25 days ago by
biwdpang
• 0
8
votes
16
replies
1.1k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 12 days ago by
bk11
★ 2.4k • written 8 weeks ago by
Sofia
• 0
4
votes
15
replies
1.6k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 4 days ago by
Gordon Smyth
★ 7.1k • written 4 months ago by
raplayer
▴ 10
10
votes
14
replies
637
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 1 day ago by
GenoMax
142k • written 7 days ago by
nicole.kavanagh
• 0
5
votes
14
replies
1.1k
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications
dorado
basecalling
nanopore
methylation
updated 27 days ago by
GenoMax
142k • written 6 weeks ago by
njornet
▴ 20
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 5 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
13
votes
14
replies
789
views
High Malat-1 expression in single cell data
single-cell
updated 12 hours ago by
t.montserrat.ayuso
▴ 40 • written 9 days ago by
carolofharvest
▴ 40
5
votes
13
replies
1.7k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 18 days ago by
ATpoint
82k • written 19 days ago by
BioinfGuru
★ 1.7k
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 14 days ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
4
votes
13
replies
967
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 21 days ago by
BioinfGuru
★ 1.7k • written 27 days ago by
matteo.levorato
• 0
5
votes
13
replies
9.3k
views
8 follow
biomaRt: Timeout on getBM().
r
biomart
ensembl
updated 27 days ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
lincaijin1994
▴ 40
12
votes
13
replies
4.4k
views
RNA-Seq DGE using PCA components as covariate
differential-gene-expression
RNA-Seq
glm
DESeq2
updated 29 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
11
votes
12
replies
1.1k
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 19 days ago by
Ram
43k • written 20 days ago by
iamsmor
• 0
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression
TPM
RNA-Seq
counts
batch-effect
21 days ago by
Ram
43k
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 20 days ago by
kjngo
• 0 • written 12.1 years ago by
Gabriel R.
★ 2.9k
30
votes
12
replies
3.9k
views
Trying to understand the maths behind one Limma function
limma
RNA-Seq
batch-effect
updated 23 days ago by
Ram
43k • written 4.0 years ago by
Mozart
▴ 330
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq
deseq2
batch-effect
updated 21 days ago by
Ram
43k • written 5.0 years ago by
Mozart
▴ 330
16
votes
12
replies
7.4k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome
perl
python3
bash
python
updated 5 days ago by
rsieber
▴ 10 • written 3.1 years ago by
Kumar
▴ 120
2
votes
11
replies
938
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 9 days ago by
jkbonfield
★ 1.2k • written 21 days ago by
me
• 0
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 21 days ago by
Ram
43k • written 5.3 years ago by
Davide Chicco
▴ 120
2
votes
11
replies
2.6k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 10 hours ago by
DGTool
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
11
replies
661
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
12 days ago by
atowns21
• 0
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 12 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
4
votes
11
replies
839
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 14 days ago by
LauferVA
4.2k • written 15 days ago by
dominickd
• 0
3
votes
11
replies
6.0k
views
Modifying R pairs() function
plotMEpairs
WGCNA
R
updated 21 days ago by
Ram
43k • written 6.4 years ago by
shania90.lk
▴ 30
25
votes
11
replies
3.8k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 14 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
11
votes
11
replies
1.2k
views
7 follow
How I know if it is a batch effect or are real differences between my controls and treatments?
RNA-seq
Transcriptomics
ComBat-seq
Batch-Effect
updated 29 days ago by
GenoMax
142k • written 4 weeks ago by
alejandro.mejiam1
▴ 10
1
vote
11
replies
5.5k
views
Truncated Bam Error
R
next-gen
sequencing
software error
updated 2 days ago by
guanghao
• 0 • written 6.1 years ago by
vivekruhela
▴ 20
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 22 days ago by
Ram
43k • written 5.0 years ago by
WouterDeCoster
47k
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 21 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 8 days ago by
cwwong13
▴ 40 • written 6.8 years ago by
lessismore
★ 1.3k
976 results • Page
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Comment: RNA seq analysis
by
ATpoint
82k
It makes absolutely no sense to conduct such an analysis. I strongly discourage you to even start with it. Results will be utterly nonsense…
Comment: Differentail gene expression results
by
swbarnes2
14k
Cross-posted: https://support.bioconductor.org/p/9158194/
Answer: Seurat V5 integration
by
Bastien Hervé
5.3k
It will depend on your context and question. I guess you will want to compare gene expression between your conditions within cell types …
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by
Adam
▴ 30
You get this error when you try to compare two data frames that have different dimensions. Try using the traceback() command to figure out …
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by
Wayne
★ 2.0k
Sorry, this was supposed to be a comment appended to the chain above. I didn't mean to post as an answer.
Comment: Exploring Diet Effects in Single-Cell RNA Sequencing
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Adam
▴ 30
> when I looked at the expression of aging marker genes, I noticed that diets sequenced in the same batch appeared more similar. How simil…
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by
DavidStreid
▴ 90
Curious if others have also benefited from Picard's [CompareSAMs][1] tool. Seems to do exactly what Madhu has requested. If the headers …
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▴ 410
The best repository is probably NCBI Organelle Resources. You can search by taxonomy and download their mt genomes. Check it out for fungi…
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142k
Good place to start looking: https://www.ncbi.nlm.nih.gov/genome/organelle/ Mitochondrial genomes may also be included in full genomes so …
Comment: Correlating Bulk Differential Expression with quantitative
by
Nicholas
• 0
Thank you! I will give it a shot
Answer: How can I analyze normalized expression data?
by
Bastien Hervé
5.3k
This has been issued a dozen times before. Have a look at Limma package. https://support.bioconductor.org/p/126817/ https://support.bioco…
Comment: Error in plotting PCA plot in seurat
by
Bastien Hervé
5.3k
Without your code, it is impossible to make any statement. Please provide the code generating that issue. By googling, here is a [similar …
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by
me
• 0
Hi, thanks for your information. I am a bit confused now. Does this mean the cram file already contained reference genome information? I in…
Comment: PseudobulkExpression.Seurat error
by
Bastien Hervé
5.3k
> None of the requested assays are present in the object Does the assay `originalexp` exist in your object `seurat_from_cds` ?
Comment: Question regarding WGCNA
by
deepak
• 0
Thank for the reply. I am running this code: # set a set of soft-thresholding powers powers = c(c(1:20), seq(from = 22, to=30, by=2)) # Ca…
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