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119,100 results • Page
1 of 2382
Sort: Rank
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0
votes
0
replies
12
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cnvpytor run problem
cnvpytor
updated 40 minutes ago by
GenoMax
146k • written 51 minutes ago by
hamideh
• 0
2
votes
5
replies
1.3k
views
VCF file generated by Gridss not recognised by VEP
NGS
variant-calling
VEP
Gridss
updated 3 hours ago by
Sunnywy0808
• 0 • written 19 months ago by
Reda
• 0
0
votes
1
reply
242
views
What is more important for Structural Variant Calling? Recall or Precision?
structural-variants
merging
precision-recall
updated 3 hours ago by
GenoMax
146k • written 6 months ago by
Luke
• 0
0
votes
1
reply
94
views
Reference genome size for genome size estimation.
tools
standard
genome
size
estimation
updated 6 hours ago by
Philipp Bayer
8.7k • written 12 hours ago by
Shakunthala Natarajan
• 0
0
votes
1
reply
132
views
Unexpected High T-Base Content in scRNA-seq Fastq Files and GC Bias Correction
Fastq
Fastqc
scRNA-seq
quality-control
updated 8 hours ago by
ATpoint
85k • written 1 day ago by
Cooper
• 0
819
votes
169
replies
156k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 25 days ago by
Biostar
3.0k • written 7.9 years ago by
Istvan Albert
101k
1
vote
3
replies
191
views
Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
DESeq2
logFC
FDR
DEGs
edgeR
updated 14 hours ago by
ATpoint
85k • written 22 hours ago by
bioinfo1994
▴ 10
0
votes
0
replies
69
views
cnv_facets run problem
_facet
cnv
1 day ago by
hamideh
• 0
0
votes
3
replies
389
views
batch correction limma package (bead based assay data)
batch-correction
updated 14 hours ago by
ATpoint
85k • written 5 days ago by
MC_J
• 0
7
votes
5
replies
2.9k
views
Limma: is it necessary to log-transform the data?
proteomics
limma
updated 1 day ago by
MC_J
• 0 • written 18 months ago by
eodmacmd
• 0
0
votes
1
reply
128
views
why do I get this error while reading single cell RNA seq data in R
scRNA-seq
updated 1 day ago by
Ram
44k • written 1 day ago by
nuorain
▴ 20
1
vote
9
replies
472
views
I need help with this scripts. Thanks.
R
1 day ago by
nuorain
▴ 20
1
vote
2
replies
222
views
Illumina RNA-seq: Overrepresented sequences are mostly in the R2 reads, not R1
illumina
rRNA
RNAseq
RNA
updated 2 days ago by
GenoMax
146k • written 2 days ago by
Umberto
▴ 10
0
votes
2
replies
241
views
Using DNA Methylation Data as Input for ChromHMM
ChromHMM
methylation
DNA
updated 1 day ago by
Ming Tommy Tang
★ 4.3k • written 2 days ago by
luminea
▴ 10
0
votes
0
replies
130
views
A question with interpreting heatmaps from limma
RNA-seq
limma
updated 1 day ago by
Ram
44k • written 2 days ago by
lhwh1208
• 0
0
votes
1
reply
163
views
STRUCTURE runs failing: core dumping and slurm exit code 10?
slurm
linux
STRUCTURE
updated 2 days ago by
GenoMax
146k • written 2 days ago by
katherinedrotos
• 0
0
votes
0
replies
131
views
Issues with RAT in CAT_pack and Optimizing Relative Abundance Calculation
metagenomics
taxonomy
mag
annotation
2 days ago by
LuciaNhu
• 0
0
votes
0
replies
130
views
Comparing whole transcriptome under one condition to the transcriptomes under other conditions
transcriptomics
2 days ago by
Texx
• 0
0
votes
0
replies
134
views
News:
Machine Learning for Multi-Omics Integration (online course) -January 13-15, 2025
Machine-Learning
Big-Data
Multi-Omics
Data-Integration
Deep-Learning
updated 1 day ago by
Ram
44k • written 2 days ago by
carlopecoraro2
★ 2.6k
1
vote
1
reply
178
views
How to make DiffBind Run Faster?
DiffBind
ATAC-seq
updated 2 days ago by
jared.andrews07
★ 17k • written 2 days ago by
B.N.
▴ 10
0
votes
0
replies
132
views
Cytoscape - stringApp terms could not be mapped to any identifier
stringApp
nodes
Cytoscape
terms
bug
2 days ago by
Jordan
• 0
0
votes
0
replies
129
views
Error While Using BSmooth in bsseq
error
bsmooth
WGBS
bsseq
methylation
2 days ago by
izmitli_biyoinformatikçi
• 0
0
votes
1
reply
159
views
validation approach for CNVs
CNV
updated 2 days ago by
Pierre Lindenbaum
164k • written 2 days ago by
heureuse
• 0
0
votes
0
replies
133
views
Advisable to perform GSVA on single cells?
GSVA
scRNA-seq
2 days ago by
bio_info
▴ 20
0
votes
0
replies
134
views
Small rna library analysis
Sirna
small-rna
updated 2 days ago by
Ram
44k • written 2 days ago by
martta95
▴ 10
0
votes
0
replies
139
views
Statistical test to be used for dataset
biostatistics
statistical-test
updated 2 days ago by
Ram
44k • written 2 days ago by
odi
▴ 10
1
vote
2
replies
254
views
Questions Regarding Normalization and Standardization in RNA-seq Differential Analysis
RNA-seq
Normalization
updated 2 days ago by
Ram
44k • written 3 days ago by
wdasda122
▴ 10
0
votes
0
replies
144
views
Boxplot with adjustment for variable
R
boxplot
2 days ago by
Bine
▴ 60
0
votes
0
replies
127
views
News:
Online Workshop - A Practical Introduction to NGS Data Analysis (December 9-11, 2024)
Workshop
Variant-Calling
RNA-Seq
Illumina
DNA-Seq
updated 2 days ago by
Ram
44k • written 2 days ago by
ecSeq Bioinformatics
• 0
0
votes
0
replies
125
views
CNVKit batch output
CNVkit
deletion
duplication
2 days ago by
aleksandra.vitkovac97
• 0
0
votes
0
replies
128
views
IGV - Load custom variant track
vcf
igv
react
2 days ago by
sadapas
• 0
0
votes
1
reply
176
views
Why are the SINEs annotated as zero when using RepeatModeler + RepeatMasker?
SINEs
Repeatmodeler
RepeatMasker
updated 2 days ago by
Michael
55k • written 2 days ago by
mut
• 0
0
votes
0
replies
132
views
ucsc table browser
ucsc
2 days ago by
daffodil
▴ 10
1
vote
2
replies
614
views
Question about various of graph format. How to get the sequence and source of a specific node?
vg
2 days ago by
chuanj8848
• 0
0
votes
0
replies
140
views
Facing problems in analysis of bisulfite sequencing data
sequencing
Bisulfite
updated 2 days ago by
GenoMax
146k • written 2 days ago by
SHREYA
• 0
1
vote
2
replies
253
views
Can anyone share with me the R code for GSEA analysis?
R
code
GSEA
2 days ago by
nuorain
▴ 20
0
votes
2
replies
266
views
extracting reads from FASTA/FASTQ file
RNA-seq
RNA
updated 3 days ago by
GenoMax
146k • written 3 days ago by
bleven
• 0
0
votes
3
replies
288
views
Different annotations for different isoforms from the same gene
metatranscriptomics
Trinity
RNA-seq
Isoform
updated 2 days ago by
Dunois
★ 2.6k • written 3 days ago by
Chikae
• 0
0
votes
0
replies
165
views
Forum:
epitope-TCR binding prediction, vaccine design
vaccine
epitope-TCR
binding
3 days ago by
Dara
• 0
0
votes
0
replies
183
views
Forum:
layoffs in biotech
layoff
biotech
3 days ago by
Dara
• 0
1
vote
1
reply
348
views
How to use lme4() to perform differential expression on bulk RNA seq data with multiple random effects?
bulkRNAseq
lme4
updated 2 days ago by
ATpoint
85k • written 3 days ago by
bioyas
▴ 20
0
votes
2
replies
247
views
Snakemake - pipeline shut down without error
snakemake
2 days ago by
bhumm
▴ 170
0
votes
1
reply
199
views
DeSeq2 filter transcripts
DeSeq2
RNA-seq
RNA
updated 3 days ago by
seidel
11k • written 3 days ago by
bleven
• 0
0
votes
0
replies
146
views
Setting up a case control with 18 VCFs in plink?
case-control
plink
WGS
3 days ago by
atopasn1
• 0
0
votes
1
reply
211
views
Aligning to transcriptome with STAR generates error in Salmon sequence length
STAR
Salmon
RNAseq
updated 3 days ago by
Dunois
★ 2.6k • written 3 days ago by
Lena
• 0
0
votes
1
reply
195
views
Gnomad result tables column meaning.
Gnomad
annotation
updated 3 days ago by
Pierre Lindenbaum
164k • written 3 days ago by
ijarne
▴ 10
1
vote
2
replies
263
views
DESeq2: adjusted p-values become NA when sub-setting samples
R
DEG
RNA-seq
DESeq2
updated 3 days ago by
GenoMax
146k • written 3 days ago by
txema.heredia
▴ 190
0
votes
1
reply
196
views
Trouble with Biopython residue depth
Proteins
Depth
Biopython
Residue
updated 3 days ago by
Wayne
★ 2.0k • written 3 days ago by
Anand KR
• 0
0
votes
2
replies
253
views
all genes have negative logFC edgeR
edgeR
updated 3 days ago by
rfran010
★ 1.3k • written 3 days ago by
xiaoyongli407
• 0
0
votes
1
reply
225
views
Split vcf file to fit tbi requirements
snp
HaplotypeCaller
vcf
gatk
updated 3 days ago by
Ram
44k • written 3 days ago by
cassandriatayfernandez
• 0
119,100 results • Page
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Answer: How can I extract 3'UTR of bacteria (Pseudomonas aeruginosa) without using R?
Answer: Center multiple pheatmap
How to get output of annotated genes from ChIPseeker tool
Answer: How to get output of annotated genes from ChIPseeker tool
Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
A: how to extract sample id with bcftools or vcftools
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Answer: VCF file generated by Gridss not recognised by VEP
by
Sunnywy0808
• 0
https://github.com/PapenfussLab/gridss/pull/618 hope it is helpful to you
Comment: What is more important for Structural Variant Calling? Recall or Precision?
by
Sunnywy0808
• 0
Hello, sorry to bother you. After reading your article, as a beginner, I have some doubts. Did you successfully genotype the vcf file of Gr…
Answer: Reference genome size for genome size estimation.
by
Philipp Bayer
8.7k
Normally you use flow cytometry-based c-values as the gold standard to compare your bioinformatics-based estimates to. Kew's c-values data…
Answer: Unexpected High T-Base Content in scRNA-seq Fastq Files and GC Bias Correction
by
ATpoint
85k
What you see is normal and expected. In 10x scRNA-seq version 3 (which this is) R1 is the CB and UMI in the first 28bp, then comes a polyT …
Comment: Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
by
ATpoint
85k
logFCs can have large standard error, especially when counts are low. The Pvalues take all that into account so for a ranking they might be…
Comment: batch correction limma package (bead based assay data)
by
ATpoint
85k
Read the user guide. It's discussed in there how to do exactly what you ask.
Comment: Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
by
bioinfo1994
▴ 10
Thank you! The guide has been really helpful in teaching me how to use EdgeR. However, I'm still puzzled about why ranking by FDR makes mor…
Answer: Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
by
Gordon Smyth
★ 7.4k
See https://bioconductor.org/packages/release/workflows/vignettes/RnaSeqGeneEdgeRQL/inst/doc/edgeRQL.html for an example workflow, which in…
Comment: samtools BGZF block error
by
Novice
▴ 10
Update: I just discovered that the error message could be due to running samtools over VPN. There was no issue with the BAM as I was able t…
Comment: why do I get this error while reading single cell RNA seq data in R
by
GenoMax
146k
It is often useful to do a quick search with the `error`. Here is one of the first search results that explains the issue: https://github.c…
Comment: batch correction limma package (bead based assay data)
by
MC_J
• 0
Many thanks! I’m planning to use Limma for batch correction, but I’ve been advised that the corrected data should generally be used only f…
Comment: I need help with this scripts. Thanks.
by
Dunois
★ 2.6k
You are welcome. I wish you a nice day too.
Comment: I need help with this scripts. Thanks.
by
nuorain
▴ 20
yes, the problem is solve luckily. Have a nice day.
Comment: Using DNA Methylation Data as Input for ChromHMM
by
Ming Tommy Tang
★ 4.3k
this tool? https://github.com/malonzm1/LuxHMM or segway https://segway.hoffmanlab.org/doc/3.0.4/index.html
Comment: I need help with this scripts. Thanks.
by
GenoMax
146k
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