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121,965 results • Page
213 of 2440
Sort: Rank
Rank
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Votes
Replies
1
vote
3
replies
1.0k
views
Requesting further clarification on interpreting relative gene expression strength
R
normalization
TPM
RNA-seq
DESeq2
updated 2.1 years ago by
ATpoint
89k • written 2.1 years ago by
Abhishek
▴ 10
1
vote
8
replies
8.2k
views
"bowtie2 died with signal 9 (KILL)" error message, having trouble figuring out how to fix my script
software-error
alignment
Assembly
bowtie2
written 6.7 years ago by
meerapprasad
▴ 10
6
votes
5
replies
3.0k
views
ChIP-seq visualization: Is it valid to do a coverage normalization in addition to applying a spike-in-derived scaling factor?
ChIP-seq
normalization
scaling-factor
coverage
spike-in
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
kalavattam
▴ 380
1
vote
2
replies
974
views
DyNet on metabolic network
metabolism
cytoscape
DyNet
2.1 years ago by
Lin
• 0
0
votes
1
reply
3.6k
views
PSMC plot (Effective population size)
next-gen
updated 2.1 years ago by
1601693223
• 0 • written 9.9 years ago by
vicky
▴ 30
2
votes
2
replies
1.1k
views
Can vg stats -a be used on a bam file?
stats
vg
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
idiaz026
▴ 10
0
votes
0
replies
692
views
problem in BIOMOD2
Random-forest
SDM
BIOMOD2
Rstudio
Machine-Learning
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
jalilahmadi1991
• 0
0
votes
1
reply
909
views
Checking a SNP as common SNP or not using UCSC genome browser
SNP
UCSC-genome-browser
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
maricom
• 0
1
vote
4
replies
1.5k
views
How to use bedtools to calculate number of reads in windows
bedtools
updated 2.1 years ago by
Pierre Lindenbaum
166k • written 2.1 years ago by
Dacheng
• 0
2
votes
1
reply
724
views
tfea.chip mouse server
transcription-factor
tfea.chip
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
Franklin
• 0
2
votes
5
replies
1.4k
views
Centrality analysis to identify TFs
TF
updated 2.1 years ago by
biofalconch
★ 1.3k • written 2.1 years ago by
Chris
▴ 360
6
votes
6
replies
2.0k
views
Integration in single cell RNAseq: What does it mean?
Single
cell
updated 2.1 years ago by
Chris
▴ 360 • written 2.1 years ago by
synat.keam
▴ 120
0
votes
1
reply
621
views
WGNCNA , hub gene identification
WGCNA
trait
hubgeneidentification
2.1 years ago by
Mehvi khan
• 0
0
votes
2
replies
2.8k
views
What is the purpose of the second cDNA in strand-specific RNA-seq
RNA-seq
updated 2.1 years ago by
rfran010
★ 1.6k • written 2.1 years ago by
Petesview
▴ 10
0
votes
0
replies
474
views
Question about umap using different numbers of pca components as initialization
umap
pca
dynamo
scRNAseq
2.1 years ago by
Zack
• 0
1
vote
1
reply
696
views
DESeq2 design formula for time - condition - donor
DESeq2
updated 2.1 years ago by
jared.andrews07
★ 19k • written 2.1 years ago by
asilvestris
• 0
3
votes
6
replies
3.0k
views
6 follow
Forum:
Is Bioinformatics a Professional Degree?
career
degree
2.1 years ago by
anasjamshed
▴ 140
0
votes
8
replies
1.8k
views
Can the DESeq2 object for paired data be set with design= ~ batch + condition?
rna-seq
deseq2
2.1 years ago by
bioinfo
▴ 160
0
votes
0
replies
471
views
Discrepancies between PCR-Based Identification and Sequence-Based Taxonomy in Bacteriophage or phage Classification
Bacteriophage
Taxonomy
Sequence-Based
PCR-Based-Identification
2.1 years ago by
dejenieshif
• 0
2
votes
4
replies
1.3k
views
Help with error using ClosetFeature() in Signac
signac
ATAC
2.1 years ago by
Chris
▴ 360
2
votes
1
reply
786
views
Human Reference Matrix for Tricycle library to predict cell cycle phases
Tricycle
scRNA-Seq
R
Single-Cell-Sequencing
Cell-Cycle
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
halimaakhter014
• 0
5
votes
7
replies
2.1k
views
Can one sample t.test be used to determine statistical significance for log2FC values?
log2FC
T.test
updated 2.1 years ago by
dsull
★ 7.7k • written 2.1 years ago by
aUser
▴ 80
7
votes
9
replies
5.4k
views
Which minimap2 parameters to set while performing mapping to avoid such mismatches
minimap2
2.1 years ago by
Mo
▴ 50
1
vote
3
replies
1.0k
views
Non-coding DNA structure prediction recomendation
Structure
DNA
prediction
updated 2.1 years ago by
bk11
★ 3.1k • written 2.1 years ago by
Phismil
▴ 20
2
votes
4
replies
5.0k
views
PolyA and PolyG sequences in FastQC/MultiQC report
multiqc
fastqc
updated 2.1 years ago by
Marco Pannone
▴ 810 • written 2.1 years ago by
kenneditodd
▴ 50
0
votes
5
replies
1.8k
views
Bowtie2 with secondary alignment option produces multiple mapping with offset and varying alignment scores
bowtie2
score
alignment
multiple-alignment
2.1 years ago by
polag01
▴ 10
0
votes
2
replies
1.4k
views
Is there a way to visualize RNA fold in R
fold
secondary
R
structure
RNA
updated 2.1 years ago by
biofalconch
★ 1.3k • written 2.1 years ago by
Serij´s
• 0
2
votes
1
reply
908
views
Inclusive vs. Separate Approaches for Gene Ontology Enrichment Analysis
Gene-Ontology
GO-terms
Enrichment
updated 2.1 years ago by
rfran010
★ 1.6k • written 2.1 years ago by
Biomed-jeh
▴ 70
2
votes
5
replies
2.2k
views
How to construct an adjacency matrix based on output of nearest neighbors search method from RANN package?
igraph
RANN
adjacency-matrix
updated 2.1 years ago by
bk11
★ 3.1k • written 2.1 years ago by
Raheleh
▴ 260
3
votes
5
replies
1.9k
views
Multiple sequence aligments - parallelisation
MSA
phylotranscriptomics
muscle
clustal
2.1 years ago by
Lada
▴ 40
2
votes
5
replies
1.7k
views
6 follow
Forum:
Biostar as a next generation version
meta
mobile-app
updated 23 months ago by
Ram
45k • written 2.1 years ago by
rj.rezwan
▴ 20
3
votes
4
replies
1.4k
views
How to Add Mutations to the sequence
mutations
NGS
sequence
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
Pratibha kadam
• 0
0
votes
1
reply
804
views
Sorting cBioPortal Oncoprinter output
cBioPortal
cancer
oncoprinter
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
ThePlaintiff
▴ 90
3
votes
7
replies
2.8k
views
Identifying transcription factors for a list of genes
transcription-factor
updated 2.0 years ago by
Ram
45k • written 2.1 years ago by
lbombini
• 0
2
votes
9
replies
2.1k
views
Forum:
open source projects looking for contributors
open-source
updated 2.1 years ago by
vincenthus
▴ 70 • written 2.1 years ago by
claudiofr
▴ 20
2
votes
4
replies
1.1k
views
Trinity output directory can be erased only with root privileges
trinity
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
langziv
▴ 70
1
vote
3
replies
1.5k
views
How to determine number of SNPs called?
Snippy
SNP
2.1 years ago by
SushiRoll
▴ 140
1
vote
2
replies
944
views
Adjusting covariate in regression model
regression
statistics
2.1 years ago by
Jonathan Yoou
▴ 70
1
vote
2
replies
882
views
Annotation of L1 from short read (single-strand) RNA
short-read
Line1
fastq
annotation
14 months ago by
Kilian
▴ 10
1
vote
6
replies
1.7k
views
Found some plasmids in my sequence. IS there any tool or process by which i can find whether there are any AMR genes within those sequence?
WGS
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
Mustafa
• 0
3
votes
6
replies
1.8k
views
BWA | SAMtools | GATK debugging help
alignment
mapping
vcf
2.1 years ago by
TheScriptOfGilgamesh
▴ 20
0
votes
5
replies
1.4k
views
How to index genome file for MethylDackel?
MethylDackel
indexing
Genome
methylation
updated 2.1 years ago by
ATpoint
89k • written 2.1 years ago by
harshraje19
▴ 50
0
votes
2
replies
1.5k
views
ClusterProfiler GeneRatio demoninator not the same for all values
enrichment-analysis
clusterprofiler
RNA-seq
deseq2
2.1 years ago by
Lily
• 0
2
votes
3
replies
1.2k
views
Trouble with breseq Bam2Cov
bamtools
bam2cov
breseq
2.1 years ago by
Freddie
• 0
0
votes
6
replies
2.0k
views
A cluster expresses two types of cells' markers in scRNA-seq
scRNA-seq
annotate
2.1 years ago by
feather-W
• 0
3
votes
3
replies
1.4k
views
Issue with dbNSFP using SnpSift
dbNSFP
SnpSift
VCF
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
aidangcruickshank
▴ 10
1
vote
3
replies
1.4k
views
Heatmap ChIP-seq average signal
chip-seq
heatmap
deeptools
updated 2.1 years ago by
Trivas
★ 1.9k • written 2.1 years ago by
Marco Pannone
▴ 810
3
votes
6
replies
1.6k
views
Output FindMarkers()
seurat
2.1 years ago by
Chris
▴ 360
5
votes
6
replies
6.6k
views
How to use the Combat-seq for batch effect removal?
batch-effect
normalization
Combat-seq
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
Yoomi
▴ 20
0
votes
8
replies
1.6k
views
Microarray DGE analysis
microarray
DGE
updated 2.1 years ago by
bk11
★ 3.1k • written 2.1 years ago by
bioinformatics
▴ 60
121,965 results • Page
213 of 2440
Recent Votes
Answer: How to create a consensus of a contig with samtools or bbmap?
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alternate allele frequency and minor allele frequency
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Answer: Gene expression equivalent of polygenic risk score ?
A: TRF output to .gff file
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arshad1292
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Comment: How to create a consensus of a contig with samtools or bbmap?
by
marongiu.luigi
▴ 760
sorry, I have mistaken samtools with spades... running `samtools view -h...` did the trick. Thank you.
Comment: Help with Ideathon
by
V K
• 0
Thank you for the response! Unfortunately this is completely independent and not part of a course. I was asking for some innovative ways to…
Answer: How to create a consensus of a contig with samtools or bbmap?
by
lieven.sterck
16k
You assembled a genome using samtools ???? that sounds very weird, if not impossible ... The header (SQ lines) is missing from your file b…
Answer: gnomad par region variants
by
benformatics
4.2k
The XX and XY counts are present on any given variants page.
Comment: Help with Ideathon
by
Mensur Dlakic
★ 30k
I don't see a single question here. Saying `I need your expert help in figuring out how I can make this analysis useful!` is too open-ended…
Comment: Differences between published differential gene expression results and own analy
by
ATpoint
89k
Please link the paper, lets see their methods. With human data it can well be that they included something like surrogate variables to damp…
Comment: Differences between published differential gene expression results and own analy
by
dsull
★ 7.7k
There are many ways to do normalization and one of the correct ways is simply to plug raw counts into deseq2 (the math that deseq2 uses to …
Comment: tximport error (medianLengthOverIsoform)
by
rfran010
★ 1.6k
Is it the version number in your data? e.g. ENST00000415118.1 vs ENST00000415118 could be causing the mismatch?
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
• 0
So is there any correct way for normalisation? I know limma recommends CPM via limma-voom and DESeq2 just takes in raw counts and does thei…
Comment: Gene expression equivalent of polygenic risk score ?
by
Picasa
▴ 690
Thanks a lot for your answer. I will check the paper.
Comment: Differences between published differential gene expression results and own analy
by
dsull
★ 7.7k
If those logFCs are different, then that's a normalization issue. The logFC is straight forward arithmetic (it's simply dividing mean of […
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
• 0
Thanks both for your input. It got me to look at the published methodologies more closely, and you guys were right. One paper that I was re…
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
• 0
Yes it does not match at all, and those genes that are common in both analysis results have very different logFC and p values
Comment: Errors with RSEM/bowtie2
by
Olivia
• 0
I am not sure what you mean by this, but I believe that is what I did. With Trinity, I matched all the paired reads together, so they shoul…
Answer: Gene expression equivalent of polygenic risk score ?
by
GouthamAtla
12k
I don't think something exists out of the box. With variants, we have a 'weight' for each variant on disease risk (obtained through large s…
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