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1,000 results • Page
1 of 20
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
11
views
GO analysis: p-value range
GO
R
1 hour ago by
sooni
▴ 20
0
votes
0
replies
24
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
2 hours ago by
Maryam
• 0
0
votes
0
replies
45
views
handling bio replicates for chromHMM
replicates
chromHMM
7 hours ago by
Hasan_Daaboul
• 0
0
votes
0
replies
48
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
8 hours ago by
DGTool
▴ 20
0
votes
0
replies
74
views
problems in installing rDock
rDock
make
Installation
Error
18 hours ago by
Rodolfo Adrián
• 0
1
vote
1
reply
293
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 1 day ago by
nguyenn6
• 0 • written 12 weeks ago by
star
▴ 10
0
votes
0
replies
96
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
100
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
1 day ago by
Moinuddin
• 0
0
votes
1
reply
142
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Jacek
▴ 20
0
votes
0
replies
111
views
How can i use ESM-1v ?
VEP
ESM-1v
1 day ago by
Meto
• 0
0
votes
0
replies
118
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
0
replies
114
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
2 days ago by
kilcdincer
▴ 10
0
votes
0
replies
138
views
genomic region of transcription factor
search
HOMER
motif
2 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
346
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
334
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
2 days ago by
hannes.bongartz
• 0
0
votes
0
replies
120
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 2 days ago by
GenoMax
142k • written 2 days ago by
yura.grabovska
▴ 90
1
vote
1
reply
180
views
constructing pangenome through psvcp
psvcp
pangenome
1 day ago by
analyst
▴ 50
0
votes
2
replies
208
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
9 hours ago by
Umer
▴ 50
0
votes
2
replies
233
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
melissachua90
▴ 70
0
votes
0
replies
120
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
2 days ago by
Varsha
• 0
0
votes
1
reply
376
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 2 days ago by
GenoMax
142k • written 2 days ago by
huxiangyulove
• 0
0
votes
0
replies
139
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
3 days ago by
O.rka
▴ 720
0
votes
4
replies
326
views
Merge clusters in Seurat UMAP
seurat
umap
2 days ago by
kilcdincer
▴ 10
0
votes
0
replies
149
views
Use of ichor CNA
Dog
CNA
genome
3 days ago by
sainavyav22
• 0
2
votes
2
replies
266
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
0
votes
0
replies
153
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
3 days ago by
Jsarria.EEAD
• 0
0
votes
1
reply
206
views
How can I calculate the OS of each patient?
overall-survival
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Pedro
• 0
0
votes
0
replies
149
views
cat-bgen fail
bgenix
updated 3 days ago by
Ram
43k • written 3 days ago by
lambard
• 0
1
vote
1
reply
200
views
API kegg - IndexError: list index out of range
kegg
API
updated 2 days ago by
Nyksubuz
▴ 20 • written 3 days ago by
mirwa.zidi93
• 0
0
votes
0
replies
140
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
3 days ago by
ebertomeup
• 0
0
votes
3
replies
280
views
Sam file Header problem
Sam
Header
problem
file
updated 2 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
saifulislam99121
• 0
0
votes
0
replies
147
views
select set of intervals that cover a genomic region
GRanges
bed
3 days ago by
ntsopoul
▴ 60
0
votes
1
reply
173
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 2 days ago by
Nyksubuz
▴ 20 • written 3 days ago by
Luqman
• 0
0
votes
4
replies
283
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
1 day ago by
mavy
▴ 10
0
votes
1
reply
175
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 3 days ago by
Michael
54k • written 4 days ago by
mgranada3
▴ 30
0
votes
1
reply
157
views
Add line under stat test
stats
R
updated 2 days ago by
Nyksubuz
▴ 20 • written 4 days ago by
Ghada
• 0
0
votes
0
replies
114
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Rodolfo Adrián
• 0
1
vote
16
replies
748
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 1 day ago by
GenoMax
142k • written 4 days ago by
hophuquy0944
• 0
0
votes
1
reply
141
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
4 days ago by
asalimih
▴ 60
0
votes
0
replies
111
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
4 days ago by
jway
• 0
0
votes
1
reply
152
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 3 days ago by
Papyrus
★ 2.9k • written 4 days ago by
yura.grabovska
▴ 90
0
votes
1
reply
153
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 3 days ago by
GenoMax
142k • written 4 days ago by
Lélé
▴ 10
0
votes
3
replies
170
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
4 days ago by
Esraa
• 0
0
votes
0
replies
98
views
ReactomeGSA
ReactomeGSA
4 days ago by
Shaimaa Gamal
▴ 10
0
votes
5
replies
289
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 3 days ago by
GenoMax
142k • written 4 days ago by
chrisk
• 0
0
votes
1
reply
174
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 3 days ago by
DGTool
▴ 20 • written 4 days ago by
iqra
• 0
0
votes
0
replies
100
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Dude
• 0
0
votes
0
replies
97
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
4 days ago by
brunofelicianodeomena
• 0
0
votes
1
reply
150
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
4 days ago by
sansan_96
▴ 90
1
vote
2
replies
233
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
3 days ago by
bioinfo
▴ 150
1,000 results • Page
1 of 20
Recent Votes
Sequence alignment on split read event such as inversion, duplication and complex nested events.
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
Comment: Add stats to the plot
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: How to add Ensembl id to cluster.markers in Seurat
How to add Ensembl id to cluster.markers in Seurat
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Recent Awards •
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Scholar
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Pierre Lindenbaum
161k
Voter
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Sara
▴ 30
Popular Question
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carlopecoraro2
★ 2.5k
Popular Question
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scideas
▴ 30
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Muhammad
• 0
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synat.keam
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jv
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Recent Replies
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
KHURRAM SHAHZAD
• 0
Thank you it works
Answer: Add stats to the plot
by
Ghada
• 0
I think this is what caused the error. we do not have group 1 and 2 in the statistical test results???? ![enter image description here][…
Answer: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot
by
GenoMax
142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
Answer: is there a tool to recover corrupted fastq files
by
Tommaso
• 0
You may also want to give a try to **FastqWiper** (https://github.com/mazzalab/fastqwiper)
Comment: Add stats to the plot
by
Ghada
• 0
Thanks. That helpful. I am getting this error data4_test <- data4.ts%>% ungroup() %>% t.test(data =.,value ~ Condition)%>% + …
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot comment here. You are asking why results between two experiments are different. I do not know without seeing the data.
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
Thank you so much for this insight. I just want to clarify another point here. I have used scRNA seq data from mice mammary epithelial cell…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Hi Pierre, I am attempting to run this code and am running into this error: (jvar) $ jvarkit vcffilterjdk -f biostar.code Dart_VCF2_Or…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim()
by
ATpoint
82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
Comment: HGVS Nomenclature of Multiple Indels found in Cis
by
LauferVA
4.2k
how has this code progressed? is it publically available? would you want to work together?
Comment: Design for complex RNA-Seq experiment using Deseq2
by
Ezequiel
• 0
I completely agree with most points. The PCA shows that the biggest driver of difference is the patients themselves, with PRE and POST time…
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