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188 results • Page
1 of 4
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0
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Generating Group/Cluster Lists from fastq files
Sequencing
RNA-seq
DNA-Seq
just now by
niruf
• 0
0
votes
0
replies
1
view
News:
Online course: Network analysis in Systems Biology with R/Bioconductor
Bioconductor
NetworkAnalysis
SystemsBiology
R
just now by
carlopecoraro2
★ 2.5k
1
vote
0
replies
17
views
Herald:
The Biostar Herald for Monday, May 20, 2024
herald
1 hour ago by
Biostar
2.8k
1
vote
3
replies
240
views
Super ehancers
enhancers
2 minutes ago by
Oburah
• 0
0
votes
0
replies
15
views
vcf phasing
beagle
WhatsHap
phasing
1 hour ago by
safeassli
▴ 10
0
votes
1
reply
67
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
updated 51 minutes ago by
Ram
43k • written 3 hours ago by
sainavyav22
• 0
0
votes
1
reply
533
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
updated 1 hour ago by
fu_entomology
▴ 40 • written 8 months ago by
juliviglino
• 0
1
vote
2
replies
113
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
identical
sequences.
updated 3 hours ago by
GenoMax
142k • written 9 hours ago by
Sony
▴ 10
0
votes
3
replies
115
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 40 minutes ago by
Ram
43k • written 5 hours ago by
Bioinformatics_begginner
▴ 20
0
votes
0
replies
39
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat
10X
scRNAseq
read10x
singlecell
5 hours ago by
ev97
▴ 20
0
votes
1
reply
77
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy
GO
R
updated 3 hours ago by
marco.barr
▴ 130 • written 6 hours ago by
sooni
▴ 20
0
votes
1
reply
60
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 2 hours ago by
GenoMax
142k • written 6 hours ago by
jinyi
• 0
0
votes
0
replies
44
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
ceRNA
ENCORI
curl
microRNA
starBase
7 hours ago by
V_Vibes
• 0
0
votes
0
replies
61
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
confounding
7 hours ago by
JorgeVallejo
▴ 20
0
votes
0
replies
58
views
transcriptome annotation
annotation
trinity
transcriptome
updated 40 minutes ago by
Ram
43k • written 7 hours ago by
Asim Bin Arshad
• 0
0
votes
4
replies
145
views
Why most genes have high padj values
deg
padj
bulkRNA
6 hours ago by
mnx0723
• 0
7
votes
14
replies
2.9k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 9 hours ago by
micah
▴ 30 • written 3.1 years ago by
kumajis
• 0
0
votes
1
reply
87
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
updated 9 hours ago by
ATpoint
82k • written 11 hours ago by
Pegasus
▴ 100
0
votes
1
reply
102
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs
PCA
GBS
LINUX
r
updated 7 hours ago by
zx8754
11k • written 12 hours ago by
Ali
• 0
0
votes
1
reply
89
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 6 hours ago by
marco.barr
▴ 130 • written 14 hours ago by
Mohamed Samir
▴ 20
0
votes
4
replies
196
views
GO analysis: p-value range
GO
R
updated 5 hours ago by
Matthias Zepper
4.6k • written 15 hours ago by
sooni
▴ 20
1
vote
0
replies
75
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
16 hours ago by
Dr.
• 0
0
votes
3
replies
199
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 3 hours ago by
GenoMax
142k • written 1 day ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
72
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
17 hours ago by
Maryam
• 0
1
vote
7
replies
353
views
Add stats to the plot
R
stats
plotting
updated 6 hours ago by
marco.barr
▴ 130 • written 1 day ago by
Ghada
• 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
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
0
votes
0
replies
85
views
handling bio replicates for chromHMM
replicates
chromHMM
22 hours ago by
Hasan_Daaboul
• 0
0
votes
0
replies
77
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
22 hours ago by
DGTool
▴ 20
0
votes
1
reply
135
views
geom_bar issue in ggplot2 with xlim()
geom_bar
ggplot2
statistics
R
updated 23 hours ago by
ATpoint
82k • written 1 day ago by
rj.rezwan
• 0
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
2
votes
0
replies
160
views
Tool:
Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap
alignment
NGMLR
1 day ago by
micah
▴ 30
0
votes
0
replies
95
views
problems in installing rDock
rDock
make
Installation
Error
1 day ago by
Rodolfo Adrián
• 0
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 1 day ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
1
vote
2
replies
699
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 1 day ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
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
0
replies
118
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
Mohamed Samir
▴ 20
0
votes
0
replies
121
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
2 days ago by
Moinuddin
• 0
0
votes
1
reply
164
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 2 days ago by
ATpoint
82k • written 2 days ago by
Jacek
▴ 20
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
0
replies
127
views
How can i use ESM-1v ?
VEP
ESM-1v
2 days ago by
Meto
• 0
0
votes
0
replies
135
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Long
• 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
0
votes
0
replies
135
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
2 days ago by
kilcdincer
▴ 10
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
0
replies
156
views
genomic region of transcription factor
search
HOMER
motif
2 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
368
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 2 days ago by
dthorbur
★ 2.0k • written 3 days ago by
BATMAN
• 0
0
votes
6
replies
358
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
2 days ago by
hannes.bongartz
• 0
0
votes
0
replies
141
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 3 days ago by
GenoMax
142k • written 3 days ago by
yura.grabovska
▴ 90
4
votes
7
replies
536
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 3 days ago by
marco.barr
▴ 130 • written 4 days ago by
diqixiaoyaoer
▴ 20
188 results • Page
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Recent Votes
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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GenoMax
142k
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safeassli
▴ 10
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to
curious
▴ 750
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Raghad
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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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