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116,825 results • Page
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0
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How/where can I get fungal mitogenome data for analysis?
fungal
mitogenome
updated 3 minutes ago by
GenoMax
142k • written 12 minutes ago by
madders73
• 0
0
votes
1
reply
84
views
How can I analyze normalized expression data?
DEseq2
RNA-seq
updated 22 minutes ago by
Bastien Hervé
5.3k • written 4 hours ago by
mnx0723
• 0
3
votes
4
replies
3.9k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 3 hours ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.4k
795
votes
167
replies
143k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
2
replies
76
views
RNA seq analysis
DESeq
RNA-seq
analysis
2 hours ago by
prifa
• 0
9
votes
3
replies
206
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 4 hours ago by
b.contreras.moreira
▴ 180 • written 21 hours ago by
ijarne
• 0
0
votes
0
replies
56
views
Chance for trained without experience
bio
updated 3 hours ago by
ATpoint
82k • written 4 hours ago by
shehab
• 0
1
vote
2
replies
99
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat
Violin-Plot
ggplot2
patchwork
4 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
45
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
5 hours ago by
Omics data mining
▴ 260
0
votes
2
replies
86
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
4 hours ago by
njornet
▴ 20
0
votes
1
reply
77
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 5 hours ago by
ATpoint
82k • written 6 hours ago by
Darya
• 0
0
votes
5
replies
142
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 3 hours ago by
Joe
21k • written 6 hours ago by
Lemonhope
• 0
0
votes
0
replies
60
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
6 hours ago by
Winter
• 0
0
votes
5
replies
160
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
31 minutes ago by
me
• 0
2
votes
11
replies
2.6k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 7 hours ago by
DGTool
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
1
reply
59
views
Error in plotting PCA plot in seurat
PCA
single-cell
seurat
scRNA
RNA
updated 30 minutes ago by
Bastien Hervé
5.3k • written 8 hours ago by
Sumeet
• 0
2
votes
1
reply
68
views
java out of memory error through beagle for imutation
beagle
java.out.of.memory
imputation
8 hours ago by
analyst
▴ 50
0
votes
0
replies
43
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
9 hours ago by
analyst
▴ 50
0
votes
0
replies
39
views
Blog:
Introduction to The Complete Sequence of a Human Genome
biotech
9 hours ago by
usa.cd.genomics
• 0
0
votes
0
replies
40
views
Blog:
Overview of Nanopore Sequencing
biotech
9 hours ago by
usa.cd.genomics
• 0
0
votes
0
replies
57
views
meffil.snp.concordance
meffil
methylation
snp_concordance
14 hours ago by
kyj222637
• 0
0
votes
1
reply
62
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 28 minutes ago by
Bastien Hervé
5.3k • written 14 hours ago by
sooni
▴ 20
1
vote
5
replies
363
views
HCL database download
HCL
updated 13 hours ago by
Ram
43k • written 4 days ago by
sooni
▴ 20
0
votes
1
reply
210
views
barcode of TCR-sequencing
barcode
updated 16 hours ago by
mizraelson
▴ 60 • written 8 days ago by
yueli7
▴ 250
0
votes
2
replies
126
views
STAR aligner error
RNA-seq
STAR
slurm
6 hours ago by
M.
▴ 30
0
votes
0
replies
60
views
monocle 3-- Could not get node in small cluster
monocle3
17 hours ago by
synat.keam
▴ 100
0
votes
2
replies
108
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
10 minutes ago by
Nicholas
• 0
1
vote
4
replies
313
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
20 hours ago by
heelpPlease
• 0
0
votes
6
replies
352
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
7 hours ago by
JACKY
▴ 140
0
votes
3
replies
211
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 19 hours ago by
Ram
43k • written 23 hours ago by
schmince
• 0
0
votes
0
replies
82
views
News:
Online course. -Time series analysis and Forecasting in R
Time-Series
Forecasting
R
Stastics
1 day ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
432
views
HLA-HD tool for genomic imputation
genomics
imputation
bash
updated 17 hours ago by
Javier
• 0 • written 3 months ago by
fra.r.silvestro
▴ 10
0
votes
1
reply
110
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Sony
▴ 10
5
votes
5
replies
234
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
12 hours ago by
Chris
▴ 280
0
votes
1
reply
115
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 1 day ago by
ATpoint
82k • written 1 day ago by
ahmad.sajad4541
• 0
1
vote
5
replies
180
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 1 day ago by
i.sudbery
19k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
133
views
student
epitranscriptomics
updated 1 day ago by
ATpoint
82k • written 1 day ago by
useriwa
• 0
0
votes
0
replies
86
views
Imputation of missing genotypes
panel
beagle
imputation
1 day ago by
analyst
▴ 50
0
votes
3
replies
148
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
6
votes
1
reply
132
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 1 day ago by
dariober
14k • written 1 day ago by
nhaus
▴ 350
2
votes
2
replies
147
views
Is therer any suggestions on mapping rate of WGBS data?
mapping
read
alignment
WGBS
12 hours ago by
Zeng Jingyu
▴ 60
1
vote
2
replies
231
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 1 day ago by
Weiwen
• 0 • written 2 days ago by
MICOS
▴ 10
0
votes
1
reply
106
views
Correlation Analysis
statistics
methylation
NGS
expression
updated 4 hours ago by
manaswwm
▴ 510 • written 1 day ago by
Researcher
▴ 30
1
vote
2
replies
155
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
23 hours ago by
robert.flynn.21
• 0
1
vote
1
reply
195
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
updated 1 day ago by
Michael
54k • written 1 day ago by
Guillermo
• 0
1
vote
5
replies
294
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
updated 6 hours ago by
Michael
54k • written 1 day ago by
qwertyuiop26
• 0
0
votes
1
reply
152
views
What is the proper way to identify the cell types of scRNAseq cluster?
scRNAseq
updated 1 day ago by
ATpoint
82k • written 2 days ago by
MAPK2
▴ 40
0
votes
2
replies
202
views
Job:
Bioinformatics Analyst - Laboratory Medicine and Pathology
job
updated 1 day ago by
Xiaofen
• 0 • written 1 day ago by
toddknutson
▴ 60
0
votes
1
reply
124
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
updated 1 day ago by
LChart
3.9k • written 1 day ago by
David
• 0
1
vote
2
replies
157
views
Where to get the following bed file?
WES
bed
reference
file
updated 1 day ago by
GenoMax
142k • written 1 day ago by
wyuan37
• 0
116,825 results • Page
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Answer: How/where can I get fungal mitogenome data for analysis?
by
alex.zaccaron
▴ 410
The best repository is probably NCBI Organelle Resources. You can search by taxonomy and download their mt genomes. Check it out for fungi…
Answer: How/where can I get fungal mitogenome data for analysis?
by
GenoMax
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 …
Comment: A question about reference genome for creating the consensus sequence
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: identifying transgene insertion site in WGS
by
Cameron.walker9900
• 0
When calling for SVs using gridds, should I use the reference genome that I added my transgene to, or should I use the unedited reference?
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…
Comment: RNA seq analysis
by
prifa
• 0
thank you for your reply Zepper, a bit clarification, I took all the samples from SRA data table, but yes from different lab and also diffe…
Comment: RNA seq analysis
by
Matthias Zepper
4.6k
That you have a varying number of replicates is not ideal ([see here why][1]), but manageable. See for example the [Specific experimental d…
Comment: Percentage coverage of reference genome by de novo genome
by
Joe
21k
OK, in that case it should be even easier as its just a single pairwise alignment, so the same advice holds.
Comment: FarmCPU - how to explain the reported 'effect'?
by
chloek88
• 0
Hi Phillip, Did you ever figure out the answer to this? I also have rMVP results with a column 'effect', values ranging from ~-1.4 to +1…
Comment: Soft-clipping read ends based on read group
by
chenl
▴ 10
Hi, Can you please share how did you clip both ends of the reads with ClipReads? Clipping form the start with `-CT "1-3"` for instance wor…
Comment: Phasing a mixture of two individuals' DNA with long reads
by
njornet
▴ 20
This is related to that other question but for now, the only thing I'm interested in is separating the three unique chromosomes, without as…
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