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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
221
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
3 days ago by
SSSJec
• 0
0
votes
3
replies
209
views
Software to separate reads from different individuals
software
development
nanopore
updated 3 days ago by
GenoMax
142k • written 3 days ago by
njornet
▴ 20
0
votes
0
replies
92
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
3 days ago by
David
• 0
0
votes
2
replies
208
views
How to update R on ubuntu
installation
update
R
apt-get
3 days ago by
Bosberg
▴ 50
0
votes
0
replies
101
views
LEfSe
LEfSe
3 days ago by
benkosta
• 0
0
votes
0
replies
88
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
3 days ago by
Sara
▴ 30
0
votes
2
replies
151
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
3 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
97
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
4 days ago by
atharvakarkare14
▴ 30
0
votes
2
replies
197
views
What should I consider as FASTA for dataset?
PDB
FASTA
3 days ago by
Nafi
• 0
0
votes
0
replies
101
views
Differential accessibility using DiffBinf
diffbind
4 days ago by
Shloka
• 0
0
votes
0
replies
93
views
vg call vs vg surject
vg
variation
graphs
updated 3 days ago by
GenoMax
142k • written 4 days ago by
aliraza3119
• 0
0
votes
1
reply
132
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 3 days ago by
GenoMax
142k • written 4 days ago by
Winter
• 0
0
votes
1
reply
206
views
Finding batch and outlayers
Pca
updated 4 days ago by
christopher medway
▴ 450 • written 4 days ago by
Tigran
• 0
2
votes
2
replies
193
views
PDB related issue
rcsb
pdb
updated 4 days ago by
noodle
▴ 580 • written 4 days ago by
Nafi
• 0
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 4 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
0
votes
1
reply
168
views
Downloading full alignments from Pfam
pfam
updated 4 days ago by
GenoMax
142k • written 4 days ago by
bef1
• 0
0
votes
0
replies
120
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 3 days ago by
dariober
14k • written 5 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
296
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 4 days ago by
ATpoint
82k • written 5 days ago by
Francesco
▴ 10
0
votes
0
replies
137
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
5 days ago by
tnminh89
▴ 10
0
votes
0
replies
141
views
Filter low express genes in microarray data
microarray
5 days ago by
Chris
▴ 260
0
votes
0
replies
565
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
6 days ago by
biocellbio
• 0
0
votes
0
replies
204
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
7 days ago by
HarperReed
• 0
1
vote
0
replies
158
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
7 days ago by
KABILAN
▴ 70
0
votes
0
replies
176
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 6 days ago by
Ram
43k • written 7 days ago by
SineWave
• 0
0
votes
0
replies
172
views
RNA-seq: full length gene
RNA-seq
updated 6 days ago by
Ram
43k • written 7 days ago by
Nargis
• 0
0
votes
0
replies
154
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
7 days ago by
turcoa1
• 0
0
votes
0
replies
165
views
Designing single-stable RNA molecules
structure
RNA
7 days ago by
Edna
• 0
0
votes
0
replies
175
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
7 days ago by
simplitia
▴ 130
1
vote
1
reply
226
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 7 days ago by
ATpoint
82k • written 7 days ago by
AaronJaime
• 0
0
votes
0
replies
160
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
7 days ago by
Emily
▴ 10
1
vote
0
replies
171
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
7 days ago by
rohitsatyam102
▴ 850
0
votes
0
replies
155
views
how to read graph_test output of monocle 3
monocle3
7 days ago by
synat.keam
▴ 100
0
votes
1
reply
499
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 7 days ago by
ginellegrenier
• 0 • written 5 months ago by
Clayton
• 0
0
votes
0
replies
152
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
8 days ago by
Aspire
▴ 330
0
votes
3
replies
301
views
Highest variable features in single cell data
single-cell
updated 6 days ago by
bk11
★ 2.4k • written 8 days ago by
carolofharvest
▴ 10
1
vote
3
replies
374
views
PCA plot
DESeq2
PCAplot
updated 4 days ago by
LauferVA
4.2k • written 8 days ago by
Aaliya
▴ 10
0
votes
0
replies
151
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
8 days ago by
4fzcgueyp5
• 0
0
votes
2
replies
262
views
Annovar using R package
Annovar
gnomAD
R
7 days ago by
DKA
▴ 40
0
votes
5
replies
369
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 7 days ago by
GenoMax
142k • written 8 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
146
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 8 days ago by
Ram
43k • written 8 days ago by
glaciya2018
• 0
0
votes
0
replies
310
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
8 days ago by
pramach1
▴ 40
0
votes
1
reply
169
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 8 days ago by
Sofia
• 0 • written 8 days ago by
mawigoj318
• 0
0
votes
0
replies
149
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
8 days ago by
salias
• 0
0
votes
5
replies
364
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 5 days ago by
Istvan Albert
100k • written 9 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
127
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 8 days ago by
Ram
43k • written 9 days ago by
newuser2024
• 0
1
vote
2
replies
246
views
alignment result
RNA-seq
samtools
hisat2
8 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
117
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
9 days ago by
Kash
▴ 110
0
votes
1
reply
165
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 9 days ago by
Mensur Dlakic
★ 27k • written 9 days ago by
benguyarenbeyaz98
• 0
2
votes
2
replies
295
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 8 days ago by
Ram
43k • written 9 days ago by
v.berriosfarias
▴ 140
2
votes
9
replies
866
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 9 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
1,000 results • Page
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Recent Votes
Answer: How many reads for WGS Sequencing?
Answer: How many reads for WGS Sequencing?
Comment: How to Calulate Allele Frequency from a VCF File?
Answer: Introduce SNPs on FASTA
Answer: how to split multi-fasta file into single fasta file named by header
How to Calulate Allele Frequency from a VCF File?
Answer: allele frequency in VCF
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Recent Replies
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
ATpoint
82k
Can you post your setup, so how many groups and their replication number? I can tell you by experience that you need even more replication …
Answer: DSEQ2 analysis
by
ATpoint
82k
The tool is called D**E**Seq2. Anyway, if your factor is `factor(conditions, levels = c("control", "mutant"))` then the first level is the …
Comment: Odd alignment question/finding
by
barslmn
★ 2.1k
Maybe it is caused by fastp. https://github.com/OpenGene/fastp/issues/506
Comment: Generating mpileup file using samtools
by
Joe
21k
It's been a long time since I did this sort of thing, but I have a vague recollection that the mpileup process was made simpler and/or roll…
Comment: Introduce SNPs on FASTA
by
Riccardo
▴ 10
Thank you very much for your answer!
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This is great also for multiline fastas
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This only works for the first line of sequences.
Answer: What purposes can TPM values be used for?
by
b.contreras.moreira
▴ 180
In case it helps: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
alifafiq1
• 0
Thank you @AT point. I was planning to use DESeq2 and use the alternate hypothesis (lessAbs) too considering that is the only package that …
Comment: Does comparing two different groups to a common third group introduce bias in th
by
ATpoint
82k
Note that by basic algebra A vs C and B vs C is the same as A vs B, so you might rethink your analysis to answer your question in a much si…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
Yes, why not? If it works for you like that, bingo!
Answer: Does comparing two different groups to a common third group introduce bias in th
by
christopher medway
▴ 450
You are testing groups A and B to a common baseline (C) - I don't see that there is anything wrong with doing that. It is a fairly common a…
Comment: HOMER on AWS
by
clairechung112
• 0
Hi. I guess it is solved by now, but as I did not find the answer immediately online, here is the answer I posted on a relevant question: h…
Answer: homer not configured properly
by
clairechung112
• 0
A late reply, but I just solved exactly the same error upon a request in the team. Please see if it helps in case anyone meets the same err…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 390
Was the spike-in a commercial product, e.g., from Zymo? Can you provide more information about what cells or DNA was spiked into your samp…
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