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116,625 results • Page
1 of 2333
Sort: Rank
Rank
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Votes
Replies
0
votes
6
replies
282
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated just now by
Alex Reynolds
35k • written 16 hours ago by
J
• 0
0
votes
0
replies
16
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
37 minutes ago by
pairedttest
▴ 10
0
votes
6
replies
389
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 45 minutes ago by
GenoMax
141k • written 3 days ago by
qudrat.nii
▴ 10
0
votes
1
reply
68
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 2 hours ago by
ATpoint
82k • written 2 hours ago by
chaco001
▴ 40
0
votes
0
replies
33
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
updated 1 hour ago by
Ram
43k • written 3 hours ago by
Guille
• 0
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
0
replies
42
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 4 hours ago by
Ram
43k • written 5 hours ago by
vanbelj
▴ 40
0
votes
0
replies
41
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 3 hours ago by
GenoMax
141k • written 6 hours ago by
hagl
▴ 10
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 6 hours ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
2
votes
2
replies
175
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
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 30 minutes ago by
Ram
43k • written 11 hours ago by
Claire Watson
▴ 60
0
votes
2
replies
158
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 30 minutes ago by
Ram
43k • written 23 hours ago by
The_PyPanda
▴ 10
0
votes
0
replies
80
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
12 hours ago by
HarperReed
• 0
3
votes
3
replies
155
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
1
vote
0
replies
60
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
60
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 34 minutes ago by
Ram
43k • written 15 hours ago by
SineWave
• 0
0
votes
0
replies
59
views
RNA-seq: full length gene
RNA-seq
updated 4 hours ago by
Ram
43k • written 15 hours ago by
Nargis
• 0
0
votes
1
reply
88
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 16 hours ago by
Jeremy Leipzig
22k • written 17 hours ago by
zihanss
• 0
0
votes
0
replies
56
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
17 hours ago by
turcoa1
• 0
3
votes
3
replies
187
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
0
votes
0
replies
71
views
Designing single-stable RNA molecules
structure
RNA
1 day ago by
Edna
• 0
0
votes
0
replies
83
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
1 day ago by
simplitia
▴ 130
0
votes
1
reply
122
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
0
votes
2
replies
177
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
2
replies
207
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 23 hours ago by
Ram
43k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
142
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
1
vote
5
replies
245
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 6 hours ago by
bk11
★ 2.4k • written 1 day ago by
starswillfade
▴ 10
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
80
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
74
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
1 day ago by
Emily
▴ 10
1
vote
0
replies
94
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
78
views
how to read graph_test output of monocle 3
monocle3
1 day ago by
synat.keam
▴ 100
0
votes
0
replies
105
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
1 day ago by
Assaf
• 0
0
votes
1
reply
410
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 1 day ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
3
votes
4
replies
241
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
1 day ago by
QX
• 0
2
votes
1
reply
163
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
91
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
1 day ago by
Aspire
▴ 300
2
votes
4
replies
241
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
updated 1 day ago by
Ram
43k • written 1 day ago by
ashaneev07
▴ 20
2
votes
3
replies
206
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
analyst
▴ 30
0
votes
1
reply
143
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
3
replies
185
views
Highest variable features in single cell data
single-cell
updated 36 minutes ago by
bk11
★ 2.4k • written 1 day ago by
Kazo
• 0
0
votes
1
reply
173
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 1 day ago by
Scooter
▴ 280 • written 2 days ago by
Akash D
▴ 40
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 1 day ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
1
vote
2
replies
222
views
PCA plot
DESeq2
PCAplot
updated 12 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
2
votes
3
replies
229
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 1 hour ago by
Ram
43k • written 1 day ago by
Ming Tommy Tang
★ 3.9k
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 1 day ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
0
votes
0
replies
115
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
2
votes
3
replies
295
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 4 days ago by
Mensur Dlakic
★ 27k • written 4 days ago by
emmanouil.a
▴ 120
0
votes
2
replies
223
views
Annovar using R package
Annovar
gnomAD
R
1 day ago by
DKA
▴ 40
0
votes
2
replies
207
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 1 day ago by
Mensur Dlakic
★ 27k • written 2 days ago by
biochugs
• 0
116,625 results • Page
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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
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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