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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
25
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 1 hour ago by
GenoMax
142k • written 2 hours ago by
Dude
• 0
0
votes
0
replies
25
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
2 hours ago by
brunofelicianodeomena
• 0
0
votes
1
reply
41
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
just now by
sansan_96
▴ 90
0
votes
1
reply
103
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 8 hours ago by
GenoMax
142k • written 9 hours ago by
bioinfo
▴ 150
0
votes
1
reply
92
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
updated 10 hours ago by
GenoMax
142k • written 11 hours ago by
melissa.joubert
• 0
0
votes
0
replies
69
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
11 hours ago by
ramiro.barrantes
• 0
0
votes
0
replies
67
views
Is there a real ground truth for CNV data?
CNV
14 hours ago by
jennyp0706
• 0
1
vote
1
reply
102
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 9 hours ago by
Ram
43k • written 14 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
60
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 14 hours ago by
GenoMax
142k • written 15 hours ago by
Bhavya
• 0
0
votes
3
replies
162
views
How to access GWAVA software of data
GWAVA
updated 15 hours ago by
GenoMax
142k • written 18 hours ago by
nonaddldy
▴ 10
0
votes
0
replies
70
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
22 hours ago by
Spring
• 0
0
votes
2
replies
141
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
19 hours ago by
IdaHao0921
• 0
0
votes
3
replies
309
views
Snakemake wrapper issue
fastqc
snakemake
updated 23 hours ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
93
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
1 day ago by
Holly
• 0
0
votes
1
reply
136
views
How to process Bulk WES data?
WES
WGS
updated 1 day ago by
GenoMax
142k • written 1 day ago by
wyuan37
• 0
0
votes
1
reply
136
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 1 day ago by
GenoMax
142k • written 1 day ago by
cedric.blais
• 0
0
votes
1
reply
125
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 1 day ago by
Ram
43k • written 1 day ago by
eking28
• 0
0
votes
0
replies
90
views
reference-free assembly error assessment tools
assembly
1 day ago by
lagartija
▴ 160
0
votes
4
replies
225
views
Galaxy StringTie error
stringtie
galaxy
17 hours ago by
trkfs
• 0
0
votes
0
replies
90
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
1 day ago by
atariw
▴ 10
1
vote
4
replies
264
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 2 hours ago by
Juke34
8.6k • written 1 day ago by
Vijith
▴ 30
0
votes
1
reply
146
views
consensus sequence calling
consensus
updated 1 day ago by
bk11
★ 2.4k • written 1 day ago by
Ghada
• 0
0
votes
0
replies
82
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
1 day ago by
JACKY
▴ 140
0
votes
0
replies
95
views
Reference panel of normals for ensembl named refgenome
Mutect2
1 day ago by
gernophil
▴ 80
1
vote
0
replies
89
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
1 day ago by
tomas4482
▴ 400
3
votes
2
replies
176
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 1 day ago by
ATpoint
82k • written 1 day ago by
jennyp0706
• 0
0
votes
0
replies
100
views
lncRNA
tcga
lncrna
1 day ago by
jain72744
▴ 10
1
vote
2
replies
344
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 1 day ago by
Ram
43k • written 2 days ago by
t.fortunato.asquini
• 0
0
votes
2
replies
194
views
Output file of samtools flagstat empty
samtools-flagstat
updated 1 day ago by
colindaven
6.4k • written 2 days ago by
ramendra.sarma
• 0
0
votes
0
replies
103
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
2 days ago by
BioinfGuru
★ 1.7k
0
votes
4
replies
372
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
1 day ago by
beginner123
• 0
0
votes
2
replies
221
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
1 day ago by
analyst
▴ 50
0
votes
1
reply
193
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 4 days ago by
Ram
43k • written 4 days ago by
Shwetha
• 0
0
votes
0
replies
158
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 4 days ago by
Ram
43k • written 4 days ago by
naomiboldon
• 0
1
vote
3
replies
269
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 4 days ago by
Ram
43k • written 4 days ago by
Omics data mining
▴ 260
0
votes
5
replies
300
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
1 day ago by
SilhouetteQ
• 0
0
votes
1
reply
179
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 4 days ago by
GenoMax
142k • written 4 days ago by
maria.soler
• 0
0
votes
2
replies
277
views
How are score_weights calculated in this code?
single-cell
3 days ago by
carolofharvest
▴ 40
0
votes
1
reply
214
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 4 days ago by
curious
▴ 750 • written 4 days ago by
SeoGyun
• 0
0
votes
0
replies
151
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
4 days ago by
Samantha
• 0
0
votes
1
reply
183
views
Microbial Signal Transduction Database
MiST
updated 4 days ago by
zx8754
11k • written 4 days ago by
Shravani
• 0
0
votes
0
replies
137
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
4 days ago by
singcell
• 0
0
votes
1
reply
207
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 4 days ago by
ATpoint
82k • written 4 days ago by
Amr
▴ 160
0
votes
2
replies
219
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
4 days ago by
jain72744
▴ 10
3
votes
1
reply
198
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 4 days ago by
dthorbur
★ 2.0k • written 5 days ago by
Eren
• 0
0
votes
0
replies
149
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
5 days ago by
Aytaç
• 0
0
votes
0
replies
164
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 4 days ago by
zx8754
11k • written 5 days ago by
curious_butterfly
• 0
0
votes
0
replies
156
views
supervised admixture
supervised
admixture
5 days ago by
RT
▴ 10
0
votes
2
replies
218
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 4 days ago by
Ram
43k • written 5 days ago by
sainavyav22
• 0
3
votes
4
replies
308
views
Truncated metadata file report from ENA Portal API
ena
python
4 days ago by
Giulia
• 0
1,000 results • Page
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Recent Votes
Comment: Overlapping Ranges within Granges object
Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: how to keep reads in a fasta file based on a seq id list in R?
Answer: The total expressed genes in RNA-Seq data
C: Re-arrange conditions in Seurat
Genome Visualization Tools
Answer: Genome Visualization Tools
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Recent Replies
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
you are on to something… if I use reduce to find the “overlaping regions” in a secon GRanges object, what do I do next?
Comment: Using ggplotly in R
by
jen
▴ 10
Thank you Jared for your response. I took a look at the documentation you provided and am trying my best to follow along, but can't seem to…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Juke34
8.6k
Right I heard there is an issue since Perl v5.36. You may have better luck using conda. Or the best way is to use the container. Or downgra…
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
Mensur Dlakic
★ 27k
pLDDT scores are stored in the so-called B-factor column in PDB files. Below the `File` ribbon select `Molecule Display` and click on `b-fa…
Comment: Genome Visualization Tools
by
dlera.lozano
▴ 10
Thank you so much
Answer: Doubt about the process of annotation, detection, identification and classificat
by
Mensur Dlakic
★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Ram
43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Ram
43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Prawesh
• 0
thanks, it's working now.
Answer: Genome Visualization Tools
by
GenoMax
142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Trivas
★ 1.8k
You need to have indexed your bam/sam file using `samtools index`
Answer: Using ggplotly in R
by
jared.andrews07
★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
Comment: Why does assigning genes with biomart give me different values than using a tran
by
GenoMax
142k
According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
Answer: RNAseq RNA content
by
noodle
▴ 580
There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Comment: Where to get the following bed file?
by
wyuan37
• 0
Hi, I emailed them and did get the bed file! Thank you so much.
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