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195 results • Page
4 of 4
Sort: replies
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0
votes
0
replies
90
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
4 days ago by
Enrique
• 0
0
votes
0
replies
73
views
Imputation advice
imputation
4 days ago by
kl
▴ 10
0
votes
0
replies
189
views
Job:
Ensembl Outreach Project Leader
ebi
embl
genomics
ensembl
4 days ago by
Ben_Ensembl
★ 2.4k
0
votes
0
replies
125
views
Job:
Ensembl Plants Senior Bioinformatician
ebi
embl
genomics
ensembl
4 days ago by
Ben_Ensembl
★ 2.4k
0
votes
0
replies
81
views
News:
Online course: DNA methylation
Pacbio
Nanopore
DnaMethylation
Evolution
4 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
81
views
Annotating single cell data automatically
cell
annotation
single
4 days ago by
Gerard
• 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
85
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
4 days ago by
manaswwm
▴ 490
0
votes
0
replies
202
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
4 days ago by
Javier
• 0
0
votes
0
replies
92
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
197
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
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
107
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
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
75
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
3 days ago by
alifafiq1
• 0
0
votes
0
replies
95
views
Merging replicates from Encode project
CHIP-seq
encode
3 days ago by
Nurken
• 0
0
votes
0
replies
87
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 2 days ago by
Ram
43k • written 3 days ago by
SHREYA
• 0
0
votes
0
replies
94
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 2 days ago by
Ram
43k • written 3 days ago by
Amélie
• 0
3
votes
0
replies
112
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
94
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
2 days ago by
ohtang7
▴ 40
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 2 days ago by
Ram
43k • written 3 days ago by
SSSJec
• 0
0
votes
0
replies
104
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
2 days ago by
Kash
▴ 110
0
votes
0
replies
130
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
2 days ago by
salias
• 0
0
votes
0
replies
247
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
2 days ago by
pramach1
▴ 40
0
votes
0
replies
129
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 2 days ago by
glaciya2018
• 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 1 day ago by
Ram
43k • written 2 days ago by
newuser2024
• 0
0
votes
0
replies
109
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
94
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
107
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
83
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
1 day ago by
Aspire
▴ 300
0
votes
0
replies
90
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
22 hours ago by
Assaf
• 0
0
votes
0
replies
67
views
how to read graph_test output of monocle 3
monocle3
22 hours ago by
synat.keam
▴ 100
1
vote
0
replies
81
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
21 hours ago by
rohitsatyam102
▴ 850
0
votes
0
replies
64
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
21 hours ago by
Emily
▴ 10
0
votes
0
replies
74
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
21 hours ago by
avocado123
• 0
0
votes
0
replies
69
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 17 hours ago by
Ram
43k • written 21 hours ago by
carlopecoraro2
★ 2.5k
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 17 hours ago by
Ram
43k • written 2 days ago by
David Langenberger
11k
0
votes
0
replies
61
views
Designing single-stable RNA molecules
structure
RNA
17 hours ago by
Edna
• 0
0
votes
0
replies
179
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
6 days ago by
DanielEB_fisk
▴ 20
0
votes
0
replies
41
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
10 hours ago by
turcoa1
• 0
0
votes
0
replies
44
views
RNA-seq: full length gene
identification
gene
full
length
8 hours ago by
Nargis
• 0
0
votes
0
replies
45
views
Running Phylogenetic Analysis With NCBI Genome
population
genetics
phylogenetic
species
sequencing
8 hours ago by
SineWave
• 0
1
vote
0
replies
45
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
7 hours ago by
KABILAN
▴ 50
0
votes
0
replies
60
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
5 hours ago by
HarperReed
• 0
2
votes
0
replies
58
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
scRNA
Machinelearning
GenerativeAI
4 hours ago by
Claire Watson
▴ 50
195 results • Page
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Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
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Comment: Is there a software that can compare phylogenetic trees to each othe (face to fa
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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…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question
by
starswillfade
▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question
by
starswillfade
▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Comment: genome assembly records not present in assembly_summary.txt
by
GenoMax
141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
Comment: what is the purpose of indexing the reference genome (Kallisto)
by
i.sudbery
19k
Specifically: If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
benformatics
3.9k
This is way easier to do solely in R now 10 years later. library(GenomicFeatures) library(rtracklayer) ## import GTF…
Answer: what is the purpose of indexing the reference genome (Kallisto)
by
dsull
★ 5.8k
I'll see if I can explain things in super simple terms (albeit with some abuse of the actual technical details) to provide a conceptual und…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
Jalil Sharif
▴ 80
The updated code in R using rtracklayer for reading a gtf file. https://github.com/jalilsharif/gtf_utr_fix_r/blob/main/gencode_utr_fix_d…
Comment: Rare Disease Variant Pathway Analysis
by
The_PyPanda
▴ 10
Thank you LauferVA, Your advice has been useful and I now a lot to think about and read. Also, I just wanted to clarify I do not ha…
Comment: CDS vs cDNA vs transcript for mapping RNA-Seq reads
by
Antonio R. Franco
★ 5.1k
You cannot do it with Kallisto either. In fact, the indexation will fail in attempting to index a genome file
Comment: PCA plot
by
ATpoint
82k
What is your question? Add details and clarity. Ask a precise question and please avoid opening more questions on the same underlying issue…
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