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115,814 results • Page
1 of 2317
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Is it better to pool samples prior to running deseq2, or should the algorithm be run separately for every pool?
deseq2
RNA-seq
updated 12 minutes ago by
swbarnes2
14k • written 3 hours ago by
Shelby
• 0
0
votes
4
replies
175
views
Expert Guidance Required for De Novo Transcriptome Analysis
Transcriptome
De-novo
updated 33 minutes ago by
Doomhammer
• 0 • written 15 hours ago by
ben@f
▴ 10
0
votes
1
reply
452
views
Downloading epigenetic and mutation data of specific TCGA BRCA samples
Mutation
RNA-Seq
TCGA
updated 1 hour ago by
aUser
▴ 30 • written 2.6 years ago by
Soura
• 0
0
votes
1
reply
87
views
Beagle Phasing and Imputation
imputation
phasing
beagle
updated 4 hours ago by
LChart
3.8k • written 7 hours ago by
Duarte Molha
▴ 240
0
votes
0
replies
39
views
Subsetting Seurat object based on list of cell barcodes
seurat
4 hours ago by
bgbs
• 0
791
votes
167
replies
138k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 8 weeks ago by
Biostar
2.5k • written 7.3 years ago by
Istvan Albert
100k
4
votes
4
replies
150
views
Differential express genes in imbalance groups
Limma
2 hours ago by
Chris
▴ 260
2
votes
1
reply
80
views
basal gene expression level
RNA-Seq
updated 6 hours ago by
LChart
3.8k • written 6 hours ago by
Francois Piumi
▴ 40
0
votes
0
replies
50
views
Biobambam vs Picard in RNA Sequencing Analysis for BAM to FASTQ
RNA-seq
Biobambam
Picard
updated 5 hours ago by
Ram
43k • written 6 hours ago by
kcarey
• 0
0
votes
0
replies
45
views
Evaluating MAST model fit using AIC
cell
single
MAST
scRNA
transcriptomics
6 hours ago by
mhale
• 0
0
votes
1
reply
100
views
Seurat 5 integration
integration
seurat
updated 7 hours ago by
jared.andrews07
★ 16k • written 9 hours ago by
sarahmanderni
▴ 100
0
votes
2
replies
102
views
scRNAseq normalization
scRNA-seq
SCT
updated 7 hours ago by
ATpoint
81k • written 8 hours ago by
sarahmanderni
▴ 100
3
votes
6
replies
1.2k
views
6 follow
Transcription Start Site
TSS
updated 8 hours ago by
el24
▴ 40 • written 23 months ago by
Fatemeh Nabizadeh
▴ 10
0
votes
0
replies
56
views
Limma contrasts - difference between single and multiple concurrent contrasts results
R
limma
updated 8 hours ago by
Ram
43k • written 9 hours ago by
shasabhi1
• 0
0
votes
0
replies
62
views
Genotype simulation
gwas
simulation
sim1000
updated 10 hours ago by
Ram
43k • written 10 hours ago by
Eliza
▴ 30
0
votes
0
replies
51
views
Tabula Sapiens and scanpy normalised expression data
scanpy
scRNA-seq
10x
normalisation
updated 10 hours ago by
Ram
43k • written 10 hours ago by
matt.a.bennett25890
• 0
4
votes
2
replies
122
views
Problem with .bed file
cygwin64
bed
PLINK
updated 7 hours ago by
Ram
43k • written 11 hours ago by
Dinmukhamed
• 0
0
votes
1
reply
168
views
compareCluster's enrichGO difference in results when stating ont = "ALL" vs NULL
enrichGO
clusterProfiler
updated 11 hours ago by
Dunois
★ 2.5k • written 20 hours ago by
TIANTHING JESTLIN
• 0
0
votes
0
replies
63
views
Remove SNPs based on MAF in Fst analysis
SNP
MAF
Fst
Popgenome
12 hours ago by
kopelol
▴ 20
3
votes
1
reply
189
views
Before or after LD clumping for PRS calculation in GWAS
GWAS
updated 13 hours ago by
Sam
★ 4.7k • written 2 days ago by
경준
▴ 20
1
vote
2
replies
216
views
Trim Galore: Automatic detection of adapters
trimgalore
6 hours ago by
Daniel
▴ 30
0
votes
0
replies
66
views
Troubleshooting a REGENIE sex-stratified GWAS
GWAS
REGENIE
13 hours ago by
s.may-wilson
▴ 40
0
votes
2
replies
147
views
Average expression of a sample in single-cell data
single-cell
rna-seq
10 hours ago by
newuser2024
• 0
0
votes
4
replies
222
views
blastn: 2.2.31+ Package: blast 2.2.31, build Jun 2 2015 10:47:46
blastn
blast
ubuntu
updated 10 hours ago by
SequenceServer
▴ 140 • written 16 hours ago by
Luca
• 0
0
votes
2
replies
138
views
nf-core/rnaseq, problem with ensembl reference
nfcore
nextflow
ensembl
rnaseq
11 hours ago by
Filip
• 0
0
votes
1
reply
101
views
Haddock 2.4
Protein
Docking
updated 16 hours ago by
dthorbur
★ 1.6k • written 16 hours ago by
Preeti
• 0
0
votes
1
reply
112
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
updated 10 hours ago by
Ram
43k • written 16 hours ago by
Learner
• 0
1
vote
1
reply
97
views
turning old shell ncbi querys into url querys
eutils
ncbi
updated 15 hours ago by
GenoMax
140k • written 16 hours ago by
Guelakais
• 0
0
votes
1
reply
442
views
ArchR Doublet Inference to Signac
Signac
scATAC-seq
ArchR
updated 17 hours ago by
fracarb8
★ 1.5k • written 13 months ago by
bioinformatics.girl
▴ 20
0
votes
2
replies
143
views
calculating mean fragment length from CollectInsertSizeMetrics(Picard) output
count2fpkm
14 hours ago by
Niharika
• 0
3
votes
10
replies
585
views
t-test in two groups, multiple rows
R
t-test
3 hours ago by
sooni
▴ 20
3
votes
4
replies
1.3k
views
sam.gz files to bam using samtools
RNA-Seq
samtools
updated 19 hours ago by
robertoalbanese.bioinfo
• 0 • written 12 months ago by
tikshyadav19
• 0
0
votes
2
replies
112
views
error in wigToBigWig while converting mappability to bedgraph
mappability
gem
bedgraph
wigToBigWig
1 hour ago by
Dora
▴ 10
0
votes
0
replies
92
views
Forum:
Field of Study in Computational Biology
Genomics
Computational-Biology
PhD
updated 10 hours ago by
Ram
43k • written 20 hours ago by
Mohammed
• 0
0
votes
2
replies
155
views
FASTA/FASTQ files of fetal Aneuploids
nipt
15 hours ago by
lolbye_1
• 0
0
votes
0
replies
99
views
comparing sc-seq combination and bulk-sequencing
bulk-sequencing
sc-sequencing
1 day ago by
润达
• 0
1
vote
1
reply
190
views
Finding homologous protein sequence using blastp led to the same sequence as output
Blastp
updated 1 day ago by
Mensur Dlakic
★ 26k • written 1 day ago by
hamid sta
▴ 10
1
vote
1
reply
143
views
Where to download DOCK 6.11?
docking
updated 1 day ago by
ATpoint
81k • written 1 day ago by
tsakeliz
• 0
0
votes
1
reply
136
views
BRIG coverage.graph issues
BRIG
sam
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
dlera.lozano
• 0
0
votes
0
replies
106
views
How to generate a comparative map using CGview?
genome
map
CGView
1 day ago by
marongiu.luigi
▴ 710
0
votes
0
replies
121
views
Advice on telling if two SNPs are on the same haplotype
ldpair
halplotype
co-occurance
gnomad
snp
1 day ago by
amy__
▴ 160
2
votes
1
reply
232
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
Clinical
TCGA-BRCA
TCGAbiolinks
Treatment-response
TCGA
updated 1 day ago by
Zhenyu Zhang
★ 1.1k • written 5 days ago by
vibhamishra017
▴ 10
1
vote
2
replies
394
views
RNA-seq differential expression across multiple tissues, 2 trials, and 2 conditions
RNA-seq
DESeq
EdgeR
Batch-effect
DEGs
17 hours ago by
BioinfGuru
★ 1.6k
1
vote
1
reply
206
views
Compute p-value, having log fold change
p-value
fold-change
updated 10 hours ago by
Ram
43k • written 2 days ago by
Ngrin
• 0
1
vote
2
replies
348
views
(ERR): "GRCh38_noalt_as" does not exist or is not a Bowtie 2 index Exiting now ...
alignment
genomics
bowtie
bowtie2
updated 11 hours ago by
Ram
43k • written 19 days ago by
Song
• 0
1
vote
2
replies
202
views
Upset plot
upsetplot
13 hours ago by
Chris
▴ 260
0
votes
1
reply
171
views
Are there any tools for mutational analysis of viruses?
virus
updated 10 hours ago by
Ram
43k • written 2 days ago by
joey
▴ 10
0
votes
5
replies
426
views
How to corrected test statistics based on the LDSC intercept?
LDSC
intercept
updated 11 hours ago by
LChart
3.8k • written 3 days ago by
Isaac
• 0
0
votes
1
reply
224
views
I can't add VAF from population for all of my variants from VCF file
vaf
vcf
genomics
gnomad
allelicfrequency
updated 2 days ago by
Arton
• 0 • written 4 days ago by
Samuel
▴ 20
0
votes
0
replies
118
views
Analyzing differentially methylated regions from Nanopore long read data?
bioinformatics
Long
read
sequencing
methylation
2 days ago by
Arton
• 0
115,814 results • Page
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Recent Votes
Comment: CAZy database has multiple family sequence...
RNA-seq differential expression across multiple tissues, 2 trials, and 2 conditions
Answer: Differential express genes in imbalance groups
Answer: Differential express genes in imbalance groups
Comment: Differential express genes in imbalance groups
Answer: Differential express genes in imbalance groups
Comment: Differential expression at pathway level
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Answer: Is it better to pool samples prior to running deseq2, or should the algorithm be
by
swbarnes2
14k
> Seems like pooling all should be statistically more robust. Yup. So put everything into the same DESeq2 object. See: https://…
Answer: Expert Guidance Required for De Novo Transcriptome Analysis
by
Doomhammer
• 0
Do you have enough clean data to assemble, for each genotypes independently? I think at first we should find the difference in transcripts …
Answer: Downloading epigenetic and mutation data of specific TCGA BRCA samples
by
aUser
▴ 30
Hi, you might have solve the problem, but for the future reference, I am writing this. The nomenclature of TCGA data set is explained here:…
Comment: error in wigToBigWig while converting mappability to bedgraph
by
Dora
▴ 10
Thank you so much for your reply! here is what I have after entering the command variableStep#chrom=NT_173277.1 Cavia porcellus strain…
Comment: Differential express genes in imbalance groups
by
Chris
▴ 260
Wow, the author of the tool reply. Thank you so much!
Comment: t-test in two groups, multiple rows
by
sooni
▴ 20
It was my mistake. I converted the dataframe to matrix. It works! Thank you!
Comment: Differential express genes in imbalance groups
by
Gordon Smyth
★ 6.9k
I do mean the quality of each sample (as measured by residual variability in the linear model, in other words by consistency with other sam…
Comment: Differential express genes in imbalance groups
by
Chris Dean
▴ 390
That sounds super interesting. I have never heard of this approach before. When you say 'sample quality weights' are you referring to dif…
Answer: Beagle Phasing and Imputation
by
LChart
3.8k
Not doable with older versions of beagle. I seem to recall that it used to be recommended to re-code the sex chromosomes of males in the re…
Answer: Differential express genes in imbalance groups
by
Gordon Smyth
★ 6.9k
Imbalanced group sizes are no problem. Just analyse the data as it is. No need to throw data away! For a human study with a large number o…
Comment: Trim Galore: Automatic detection of adapters
by
Daniel
▴ 30
Got it, this clears things up. Thank you!
Answer: basal gene expression level
by
LChart
3.8k
I haven't seen any reliable way to estimate absolute RNA concentrations from sequencing data. Methods have been developed using [housekeepi…
Answer: Seurat 5 integration
by
jared.andrews07
★ 16k
You are still free to change whichever parameters you want for whichever method you're using. See `?IntegrateLayers` and whichever method y…
Answer: scRNAseq normalization
by
ATpoint
81k
It's perfectly fine to use log-transformation. The advantages of these more complicated methods usually depend on context and also on the w…
Answer: scRNAseq normalization
by
dsull
★ 5.6k
No, your log-transform might indeed be ok (or even better) for your analysis of interest. See https://www.nature.com/articles/s41592-023…
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