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196 results • Page
3 of 4
Sort: replies
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Votes
Replies
0
votes
1
reply
281
views
Could you please assist in identifying this cluster?
single-cell
updated 6 days ago by
Ram
43k • written 6 days ago by
Kazo
• 0
1
vote
1
reply
398
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
6 days ago by
renan.igor
• 0
0
votes
1
reply
261
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 6 days ago by
GenoMax
141k • written 6 days ago by
bioyas
▴ 10
2
votes
1
reply
286
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 6 days ago by
GenoMax
141k • written 6 days ago by
rebecca.calvo
• 0
1
vote
1
reply
296
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie
Cufflinks
Ballgown
DESeq2
updated 6 days ago by
Ram
43k • written 6 days ago by
Nina
• 0
1
vote
1
reply
254
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray
HumanHT-12v4
Illumina
updated 5 days ago by
Gordon Smyth
★ 7.0k • written 6 days ago by
Bioinformatician
• 0
1
vote
1
reply
413
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 5 days ago by
Gordon Smyth
★ 7.0k • written 7 days ago by
Chris
▴ 260
0
votes
1
reply
174
views
homology modelling using swiss model
homology-modeling
swiss-model
updated 3 days ago by
colindaven
6.4k • written 4 days ago by
Ayush
• 0
0
votes
1
reply
128
views
FAM FILE
file
Fam
3 days ago by
Eleonora
• 0
0
votes
1
reply
148
views
RNA-seq bacteria contamination
RNA-seq
updated 3 days ago by
GenoMax
141k • written 3 days ago by
sh
• 0
0
votes
1
reply
121
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 3 days ago by
ATpoint
82k • written 3 days ago by
enanoide
• 0
0
votes
1
reply
127
views
tbtool
tbtool
updated 3 days ago by
Ram
43k • written 3 days ago by
Raman
• 0
0
votes
1
reply
142
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 3 days ago by
Ram
43k • written 3 days ago by
Cameron.walker9900
• 0
1
vote
1
reply
152
views
WGCNA preservation analysis
WGCNA
preservation
updated 2 days ago by
Michael
54k • written 2 days ago by
michael.flower.14
▴ 180
0
votes
1
reply
126
views
Plots for DNA methylation data
plots
DNA
methylation
updated 2 days ago by
GenoMax
141k • written 2 days ago by
sarahawan92
▴ 10
0
votes
1
reply
152
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Srinka
▴ 20
1
vote
1
reply
163
views
Failed kmer content
kmer
illumina
ngs
updated 2 days ago by
Ram
43k • written 3 days ago by
Kasturi
• 0
0
votes
1
reply
128
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 2 days ago by
bk11
★ 2.4k • written 2 days ago by
Susmita Mandal
▴ 110
0
votes
1
reply
150
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 2 days ago by
bk11
★ 2.4k • written 2 days ago by
alphaflylizard
• 0
1
vote
1
reply
140
views
Including plasmid in transcriptome assemblies
Bacteria
BOWTIE2
Transcriptomics
STAR
updated 2 days ago by
GenoMax
141k • written 2 days ago by
heelpPlease
• 0
3
votes
1
reply
208
views
Seurat merge and batch correction
Seurat
updated 2 days ago by
Ram
43k • written 3 days ago by
sooni
▴ 20
1
vote
1
reply
177
views
Herald:
The Biostar Herald for Tuesday, April 23, 2024
herald
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
Biostar
2.7k
0
votes
1
reply
197
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 2 days ago by
Istvan Albert
100k • written 3 days ago by
Abeer
• 0
0
votes
1
reply
139
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
benguyarenbeyaz98
• 0
0
votes
1
reply
138
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 1 day ago by
Sofia
• 0 • written 1 day ago by
mawigoj318
• 0
0
votes
1
reply
152
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 1 day ago by
Scooter
▴ 280 • written 1 day ago by
Akash D
▴ 40
0
votes
1
reply
126
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 23 hours ago by
b.contreras.moreira
▴ 170 • written 1 day ago by
Broccoli
• 0
2
votes
1
reply
145
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 21 hours ago by
Adrian Altenhoff
★ 1.1k • written 1 day ago by
hemantcnaik
• 0
0
votes
1
reply
151
views
PCA plot
DESeq2
PCAplot
updated 16 hours ago by
jkim
▴ 170 • written 1 day ago by
Aaliya
▴ 10
0
votes
1
reply
387
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 15 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
1
vote
1
reply
118
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
updated 10 hours ago by
Ram
43k • written 17 hours ago by
Francesco
▴ 10
0
votes
1
reply
147
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 10 hours ago by
Ram
43k • written 1 day ago by
Ming Tommy Tang
★ 3.9k
0
votes
1
reply
81
views
Rare Disease Variant Pathway Analysis
Pathway
analysis
updated 8 hours ago by
LauferVA
4.2k • written 8 hours ago by
The_PyPanda
▴ 10
0
votes
1
reply
45
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 2 hours ago by
Jeremy Leipzig
22k • written 2 hours ago by
zihanss
• 0
0
votes
0
replies
75
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
2 days ago by
alifafiq1
• 0
0
votes
0
replies
120
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 1 day ago by
Ram
43k • written 1 day ago by
glaciya2018
• 0
0
votes
0
replies
110
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 1 day ago by
Ram
43k • written 1 day ago by
newuser2024
• 0
0
votes
0
replies
106
views
News:
hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models
GLM
R
updated 1 day ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
93
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 1 day ago by
Ram
43k • written 2 days ago by
Jeyong
• 0
0
votes
0
replies
159
views
Forum:
Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation
scRNA
llm
3 days ago by
yxwucq
• 0
0
votes
0
replies
106
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 3 days ago by
Ram
43k • written 3 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
273
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 3 days ago by
Ram
43k • written 14 months ago by
Oak
▴ 10
0
votes
0
replies
194
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 3 days ago by
Ram
43k • written 3 days ago by
Oak
▴ 10
0
votes
0
replies
97
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
1 day ago by
4fzcgueyp5
• 0
0
votes
0
replies
91
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 3 days ago by
Ram
43k • written 3 days ago by
sansan_96
▴ 80
0
votes
0
replies
202
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
3 days ago by
Javier
• 0
0
votes
0
replies
84
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
3 days ago by
manaswwm
▴ 490
0
votes
0
replies
82
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
3 days ago by
feather-W
• 0
0
votes
0
replies
196
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 6 days ago by
Ram
43k • written 6 days ago by
Dinmukhamed
• 0
0
votes
0
replies
79
views
Annotating single cell data automatically
cell
annotation
single
3 days ago by
Gerard
• 0
196 results • Page
3 of 4
Recent Votes
cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
Answer: Seurat merge and batch correction
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
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Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
Thank you for replying Pierre. I first added a third column to the SNP bed file, so that I would get a range of 1 for each SNP awk 'B…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
> using bcftools Show us what you tried
Answer: gvcf joint calling
by
Jeremy Leipzig
22k
> Hi, guys, there is a question about the genomic gVCF file. I wonder > that since gVCF contains the non-var block records, why after merge…
Comment: Missing protein (VEGF-A) in String db
by
shalespringer
• 0
Thank you for replying here; this helped me figure out why MAPK10 was missing from my results. It was also marked as a pseudogene in the En…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
These are the first lines of the output: (Please is it normal to have NA in the P value column ?) CHR …
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
So I used the barcodes that I created (combos of positions 1-10 and 11-20) and I obtained similar alignment stats as the paper I pulled the…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thank you so much, it actually worked!
Answer: Rare Disease Variant Pathway Analysis
by
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4.2k
Hi @efc1e545 , First a caveat. the information we most need in order to help guide you to a successful conclusion is not provided in thi…
Answer: Sequence read length shorter than flow cell specification
by
swbarnes2
14k
The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unle…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Comment: Annovar using R package
by
DKA
▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
ATpoint
82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
by
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82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
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by
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• 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
kilcdincer
▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
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