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186 results • Page
3 of 4
Sort: Views
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Views
Votes
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0
votes
0
replies
197
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 4 days ago by
Ram
43k • written 4 days ago by
Oak
▴ 10
3
votes
3
replies
194
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 4 days ago by
Mensur Dlakic
★ 27k • written 4 days ago by
c_u
▴ 520
0
votes
2
replies
192
views
Result of running of p3_in.pl
primer3
updated 4 days ago by
GenoMax
141k • written 4 days ago by
nasri
• 0
0
votes
0
replies
191
views
Job:
Ensembl Outreach Project Leader
ebi
embl
genomics
ensembl
4 days ago by
Ben_Ensembl
★ 2.4k
3
votes
3
replies
186
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 23 hours ago by
swbarnes2
14k • written 1 day ago by
M
• 0
1
vote
1
reply
184
views
Herald:
The Biostar Herald for Tuesday, April 23, 2024
herald
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
Biostar
2.7k
0
votes
3
replies
180
views
Highest variable features in single cell data
single-cell
updated 26 minutes ago by
bk11
★ 2.4k • written 1 day ago by
Kazo
• 0
6
votes
3
replies
180
views
Interpretting IGV output
IGV
updated 4 days ago by
Carlo Yague
8.7k • written 4 days ago by
analyst
▴ 30
0
votes
2
replies
177
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
4 days ago by
sainavyav22
• 0
0
votes
2
replies
175
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Begonia_pavonina
▴ 150
0
votes
1
reply
175
views
homology modelling using swiss model
homology-modeling
swiss-model
updated 4 days ago by
colindaven
6.4k • written 5 days ago by
Ayush
• 0
2
votes
2
replies
174
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 9 hours ago by
dsull
★ 5.8k • written 16 hours ago by
Aaliya
▴ 10
0
votes
1
reply
172
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 1 day ago by
Scooter
▴ 280 • written 2 days ago by
Akash D
▴ 40
1
vote
1
reply
167
views
Failed kmer content
kmer
illumina
ngs
updated 3 days ago by
Ram
43k • written 3 days ago by
Kasturi
• 0
2
votes
1
reply
162
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 1 day ago by
Adrian Altenhoff
★ 1.1k • written 2 days ago by
hemantcnaik
• 0
0
votes
0
replies
162
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
2
replies
157
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 20 minutes ago by
Ram
43k • written 22 hours ago by
The_PyPanda
▴ 10
0
votes
1
reply
156
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 3 days ago by
GenoMax
141k • written 3 days ago by
Srinka
▴ 20
1
vote
1
reply
156
views
WGCNA preservation analysis
WGCNA
preservation
updated 3 days ago by
Michael
54k • written 3 days ago by
michael.flower.14
▴ 180
0
votes
1
reply
152
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 3 days ago by
bk11
★ 2.4k • written 3 days ago by
alphaflylizard
• 0
3
votes
3
replies
148
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 9 hours ago by
GenoMax
141k • written 12 hours ago by
sapuizait
▴ 10
0
votes
1
reply
149
views
RNA-seq bacteria contamination
RNA-seq
updated 4 days ago by
GenoMax
141k • written 4 days ago by
sh
• 0
0
votes
1
reply
147
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
1
vote
1
reply
144
views
Including plasmid in transcriptome assemblies
Bacteria
BOWTIE2
Transcriptomics
STAR
updated 3 days ago by
GenoMax
141k • written 3 days ago by
heelpPlease
• 0
0
votes
1
reply
143
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 4 days ago by
Ram
43k • written 4 days ago by
Cameron.walker9900
• 0
0
votes
1
reply
142
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 1 day ago by
b.contreras.moreira
▴ 170 • written 1 day ago by
Broccoli
• 0
0
votes
1
reply
141
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 2 days ago by
Sofia
• 0 • written 2 days ago by
mawigoj318
• 0
1
vote
1
reply
141
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
updated 1 day ago by
Ram
43k • written 1 day ago by
Francesco
▴ 10
0
votes
0
replies
139
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 5 days ago by
Ram
43k • written 5 days ago by
sainavyav22
• 0
0
votes
0
replies
138
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
5 days ago by
rthapa
▴ 90
0
votes
1
reply
133
views
Plots for DNA methylation data
plots
DNA
methylation
updated 3 days ago by
GenoMax
141k • written 3 days ago by
sarahawan92
▴ 10
0
votes
1
reply
133
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 3 days ago by
bk11
★ 2.4k • written 3 days ago by
Susmita Mandal
▴ 110
0
votes
0
replies
133
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
5 days ago by
Mamatha Y S
• 0
0
votes
0
replies
132
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
2 days ago by
salias
• 0
0
votes
1
reply
131
views
FAM FILE
file
Fam
4 days ago by
Eleonora
• 0
0
votes
1
reply
131
views
tbtool
tbtool
updated 4 days ago by
Ram
43k • written 4 days ago by
Raman
• 0
0
votes
0
replies
130
views
News:
upcoming online statistical courses
Statistics
R
Data-Analysis
updated 5 days ago by
Ram
43k • written 6 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
130
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 2 days ago by
Ram
43k • written 2 days ago by
glaciya2018
• 0
0
votes
0
replies
127
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 4 days ago by
Carlo Yague
8.7k • written 4 days ago by
Atul K.
• 0
0
votes
1
reply
126
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 4 days ago by
ATpoint
82k • written 4 days ago by
enanoide
• 0
0
votes
0
replies
126
views
Job:
Ensembl Plants Senior Bioinformatician
ebi
embl
genomics
ensembl
4 days ago by
Ben_Ensembl
★ 2.4k
0
votes
1
reply
121
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 1 day ago by
ATpoint
82k • written 1 day ago by
AaronJaime
• 0
3
votes
0
replies
116
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 3 days ago by
Ram
43k • written 3 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
114
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
112
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 2 days ago by
Ram
43k • written 2 days ago by
newuser2024
• 0
0
votes
0
replies
112
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
updated 1 day ago by
Ram
43k • written 2 days ago by
David Langenberger
11k
0
votes
0
replies
109
views
News:
hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models
GLM
R
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
108
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 4 days ago by
Ram
43k • written 4 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
105
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
2 days ago by
Kash
▴ 110
0
votes
0
replies
105
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
1 day ago by
Assaf
• 0
186 results • Page
3 of 4
Recent Votes
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Comment: PCA plot
C: RNA seq library size
RNA seq library size
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
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Recent Replies
Comment: Highest variable features in single cell data
by
bk11
★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq
by
GenoMax
141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq
by
dsull
★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
ATpoint
82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon
by
i.sudbery
19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
by
bk11
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
by
GenoMax
141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely aligning in regions wh…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq
by
pinheirofabiano
▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
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