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188 results • Page
2 of 4
Sort: Views
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Views
Votes
Replies
0
votes
4
replies
333
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 3 days ago by
Tony
• 0 • written 4 days ago by
vk
▴ 10
3
votes
1
reply
332
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 5 days ago by
dariober
14k • written 6 days ago by
Holly
▴ 30
1
vote
5
replies
323
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 3 days ago by
Ram
43k • written 4 days ago by
manuelmourato25
• 0
1
vote
2
replies
321
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 19 hours ago by
Tommaso
• 0 • written 3 months ago by
pt.taklifi
▴ 60
1
vote
1
reply
316
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 1 day ago by
nguyenn6
• 0 • written 3 months ago by
star
▴ 10
0
votes
5
replies
312
views
calculating genomic coverage/ base overlap in R
genomics
updated 2 days ago by
1769mkc
★ 1.2k • written 5 days ago by
Xbox_27
• 0
2
votes
4
replies
311
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
5 days ago by
Esraa
• 0
0
votes
2
replies
302
views
Traveler with Infernal mapping failed
r2dt
updated 1 day ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 0
1
vote
4
replies
300
views
Add stats to boxplot in R
stats
R
4 days ago by
Ghada
• 0
1
vote
4
replies
300
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
4 days ago by
Arton
▴ 10
1
vote
3
replies
299
views
Using ggplotly in R
ggplot
ggplotly
updated 5 days ago by
jared.andrews07
★ 16k • written 5 days ago by
jen
▴ 10
3
votes
3
replies
298
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 6 days ago by
Ram
43k • written 20 days ago by
Adyasha
• 0
0
votes
5
replies
292
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 4 days ago by
GenoMax
142k • written 5 days ago by
chrisk
• 0
0
votes
4
replies
291
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
18 hours ago by
Bibi
• 0
2
votes
3
replies
291
views
Finding variants within a subset of a BAM file
variant
calling
5 days ago by
ramiro.barrantes
• 0
2
votes
5
replies
290
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 6 days ago by
Philipp Bayer
8.5k • written 6 days ago by
林明德
• 0
3
votes
2
replies
289
views
imputation through beagle
panel
beagle
reference
imputation
6 days ago by
analyst
▴ 50
0
votes
4
replies
287
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
2 days ago by
mavy
▴ 10
1
vote
3
replies
287
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 3 days ago by
Ram
43k • written 5 days ago by
kuttibiotech2009
▴ 30
0
votes
2
replies
285
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
1 day ago by
Ezequiel
• 0
1
vote
3
replies
284
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 3 days ago by
GenoMax
142k • written 6 days ago by
ohtang7
▴ 40
0
votes
3
replies
282
views
Sam file Header problem
Sam
Header
problem
file
updated 3 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
saifulislam99121
• 0
2
votes
4
replies
277
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 4 days ago by
yura.grabovska
▴ 90 • written 4 days ago by
ev97
▴ 20
2
votes
2
replies
275
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 3 days ago by
Ram
43k • written 3 days ago by
txema.heredia
▴ 130
2
votes
2
replies
275
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
20 minutes ago by
beantkapoor16
▴ 10
1
vote
5
replies
273
views
Annotating file using bcftools
annotation
plink
bcftools
4 days ago by
kl
▴ 10
1
vote
2
replies
272
views
How to interpret infinite odds ratio?
statistics
6 days ago by
Lukas
• 0
0
votes
3
replies
271
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 5 days ago by
noodle
▴ 580 • written 6 days ago by
doramora
▴ 10
0
votes
4
replies
269
views
Galaxy StringTie error
stringtie
galaxy
6 days ago by
trkfs
• 0
0
votes
3
replies
265
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 10 hours ago by
nd48
▴ 20 • written 3 days ago by
Umer
▴ 50
2
votes
3
replies
258
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 3 days ago by
Ram
43k • written 4 days ago by
sooni
▴ 20
0
votes
1
reply
251
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 6 days ago by
Ram
43k • written 10 days ago by
Nikki
• 0
3
votes
3
replies
251
views
getting exon coordinates
genomics
updated 4 days ago by
Ram
43k • written 4 days ago by
Xbox_27
• 0
0
votes
2
replies
251
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
melissachua90
▴ 70
1
vote
1
reply
250
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
4 days ago by
ramiro.barrantes
• 0
0
votes
4
replies
248
views
Sequencing Depth (Read Depth) Calculations
depth
4 days ago by
LucisTheFather
• 0
0
votes
2
replies
247
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 2 days ago by
LauferVA
4.2k • written 2 days ago by
ijarne
• 0
0
votes
2
replies
241
views
Trimming tool
Trimmer
tool
updated 2 days ago by
ntsopoul
▴ 60 • written 2 days ago by
GeneC
• 0
1
vote
3
replies
240
views
Super ehancers
enhancers
2 minutes ago by
Oburah
• 0
2
votes
4
replies
239
views
Help with IGV abbreviation
igv
updated 5 days ago by
Ram
43k • written 6 days ago by
GeneC
• 0
3
votes
3
replies
238
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 4 days ago by
ATpoint
82k • written 5 days ago by
Alexandra
• 0
1
vote
2
replies
236
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
4 days ago by
MarcosCosta
• 0
1
vote
2
replies
236
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
4 days ago by
bioinfo
▴ 150
0
votes
2
replies
232
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
4 days ago by
Chen
• 0
1
vote
5
replies
231
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 5 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
biology_inform
▴ 50
2
votes
1
reply
230
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 1 day ago by
Gordon Smyth
★ 7.2k • written 2 days ago by
marineandriot
• 0
0
votes
3
replies
223
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 6 days ago by
GenoMax
142k • written 6 days ago by
RNAseqer
▴ 270
2
votes
3
replies
221
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 5 days ago by
Ram
43k • written 5 days ago by
Prawesh
• 0
1
vote
1
reply
218
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 4 days ago by
Ram
43k • written 4 days ago by
m90
▴ 30
0
votes
3
replies
215
views
How to access GWAVA software of data
GWAVA
updated 6 days ago by
GenoMax
142k • written 6 days ago by
nonaddldy
▴ 10
188 results • Page
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The Biostar Herald for Monday, May 20, 2024
ClusterProfiler : What is GeneRatio and BgRatio?
A: ClusterProfiler : What is GeneRatio and BgRatio?
A: ClusterProfiler : What is GeneRatio and BgRatio?
C: Cleaning RNA-Seq data from rRNA
Answer: How to find identical sequences in genome fasta file (by Python or any possible
Merging/Concatenating Vcf Files
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Recent Replies
Comment: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
Hello, just wanted to check in if the code has been fixed yet? Thank you.
Comment: Super ehancers
by
jared.andrews07
★ 16k
Based on the [source code](https://bitbucket.org/young_computation/rose/src/feb35cb1d9556a76f8ac1f51521539bb30651343/ROSE_utils.py?at=maste…
Comment: HGVS Nomenclature of Multiple Indels found in Cis
by
Ram
43k
They're not addressing the actual question, just saying something tangentially related. It looks like their understanding of both consensus…
Comment: Super ehancers
by
Oburah
• 0
Hello, i encountered this problem when running ROSE, Do anyone know how to solve it? python2.7 ROSE_main.py -g HG38 -i /home/hesborn/Desk…
Answer: How to generate an Upset plot in R to plot the shared variants between cell free
by
zx8754
11k
Try this example: library(UpSetR) #example input, 4 samples, 250 variants set.seed(1); d <- data.frame(matrix(sample…
Answer: Illumina methylation EPIC V2 array
by
fu_entomology
▴ 40
We have been using SeSAMe, it works well for the most part. They have an enrichment tool called KnowYourCG. You can check it out their vign…
Answer: How to find identical sequences in genome fasta file (by Python or any possible
by
GenoMax
142k
> My final purpose are find and remove any identical sequences present in my genome fasta file. You can use `clumpify.sh` from BBMap suite…
Comment: GO analysis: Indicate genes corresponding to the pathway
by
marco.barr
▴ 130
I think you have set a filter to get these pahways upstream from the DEG results. You should extract the IDs or names of the genes that you…
Comment: GATK Structural Variants Pipeline - Steps
by
Bioinformatics_begginner
▴ 20
Thank you for the response, I mean those tools aren't all the steps from fasta to vcf. Would be key understanding the aligner, reference us…
Comment: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
GenoMax
142k
Please accept the answer (green check mark) to provide closure to this thread.
Answer: GATK Structural Variants Pipeline - Steps
by
Pierre Lindenbaum
161k
> A structural variation pipeline for short-read sequencing https://github.com/broadinstitute/gatk-sv
Comment: GATK Structural Variants Pipeline - Steps
by
DGTool
▴ 20
If it is just the tools that they used which you are looking for, the first link in the overview section of that page leads to the followin…
Comment: GO analysis: p-value range
by
Matthias Zepper
4.6k
It is just a warning that you add a new scale to a ggplot2 plot, that already has an existing one, which will get replaced. Nothing to worr…
Comment: GO analysis: p-value range
by
marco.barr
▴ 130
If you write me the code you used I can help you more
Comment: GO analysis: p-value range
by
sooni
▴ 20
When I run the code, the following message appears: Scale for y is already present. Adding another scale for y, which will replace…
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