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187 results • Page
4 of 4
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Views
Votes
Replies
0
votes
0
replies
97
views
Merging replicates from Encode project
CHIP-seq
encode
3 days ago by
Nurken
• 0
0
votes
0
replies
95
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 3 days ago by
Ram
43k • written 4 days ago by
Amélie
• 0
1
vote
0
replies
95
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
1 day ago by
rohitsatyam102
▴ 850
0
votes
0
replies
94
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
3 days ago by
ohtang7
▴ 40
0
votes
0
replies
94
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 2 days ago by
Ram
43k • written 2 days ago by
Jeyong
• 0
0
votes
0
replies
91
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
1 day ago by
Aspire
▴ 300
0
votes
0
replies
92
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 4 days ago by
Ram
43k • written 4 days ago by
sansan_96
▴ 80
0
votes
0
replies
91
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
4 days ago by
Enrique
• 0
0
votes
1
reply
91
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 17 hours ago by
Jeremy Leipzig
22k • written 17 hours ago by
zihanss
• 0
3
votes
0
replies
89
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 50 minutes ago by
Ram
43k • written 11 hours ago by
Claire Watson
▴ 60
0
votes
0
replies
88
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 3 days ago by
Ram
43k • written 3 days ago by
SHREYA
• 0
0
votes
0
replies
86
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
4 days ago by
manaswwm
▴ 490
0
votes
0
replies
86
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 3 days ago by
Ram
43k • written 3 days ago by
SSSJec
• 0
0
votes
0
replies
84
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
1 day ago by
avocado123
• 0
0
votes
0
replies
84
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
1 day ago by
simplitia
▴ 130
0
votes
0
replies
83
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
12 hours ago by
HarperReed
• 0
0
votes
0
replies
82
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
4 days ago by
feather-W
• 0
0
votes
0
replies
82
views
News:
Online course: DNA methylation
Pacbio
Nanopore
DnaMethylation
Evolution
4 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
82
views
Annotating single cell data automatically
cell
annotation
single
4 days ago by
Gerard
• 0
0
votes
0
replies
81
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
4 days ago by
Biostars2200
• 0
0
votes
0
replies
81
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
79
views
how to read graph_test output of monocle 3
monocle3
1 day ago by
synat.keam
▴ 100
0
votes
1
reply
74
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 3 hours ago by
ATpoint
82k • written 3 hours ago by
chaco001
▴ 40
0
votes
0
replies
76
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
3 days ago by
alifafiq1
• 0
0
votes
0
replies
75
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
1 day ago by
Emily
▴ 10
0
votes
0
replies
74
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
4 days ago by
sativus
▴ 20
0
votes
0
replies
73
views
Designing single-stable RNA molecules
structure
RNA
1 day ago by
Edna
• 0
0
votes
0
replies
73
views
Imputation advice
imputation
4 days ago by
kl
▴ 10
0
votes
0
replies
63
views
RNA-seq: full length gene
RNA-seq
updated 5 hours ago by
Ram
43k • written 15 hours ago by
Nargis
• 0
1
vote
0
replies
61
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
14 hours ago by
KABILAN
▴ 50
0
votes
0
replies
61
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 54 minutes ago by
Ram
43k • written 15 hours ago by
SineWave
• 0
0
votes
0
replies
58
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
17 hours ago by
turcoa1
• 0
0
votes
0
replies
45
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 4 hours ago by
GenoMax
141k • written 6 hours ago by
hagl
▴ 10
0
votes
0
replies
45
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 5 hours ago by
Ram
43k • written 5 hours ago by
vanbelj
▴ 40
0
votes
0
replies
37
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
updated 2 hours ago by
Ram
43k • written 3 hours ago by
Guille
• 0
0
votes
0
replies
20
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
58 minutes ago by
pairedttest
▴ 10
0
votes
0
replies
9
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
10 minutes ago by
biocellbio
• 0
187 results • Page
4 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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141k
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Recent Replies
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Alex Reynolds
35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
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?
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