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116,627 results • Page
1 of 2333
Sort: Rank
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Votes
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0
votes
0
replies
15
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
1 hour ago by
O.rka
▴ 710
0
votes
1
reply
64
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
updated 2 hours ago by
Gordon Smyth
★ 7.0k • written 4 hours ago by
pairedttest
▴ 10
2
votes
6
replies
1.8k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 2 hours ago by
Ram
43k • written 2.3 years ago by
SYOSY
▴ 10
0
votes
0
replies
55
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
3 hours ago by
biocellbio
• 0
4
votes
8
replies
360
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
3 hours ago by
J
▴ 10
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
3
votes
6
replies
425
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 4 hours ago by
GenoMax
141k • written 3 days ago by
qudrat.nii
▴ 10
1
vote
1
reply
94
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 6 hours ago by
ATpoint
82k • written 6 hours ago by
chaco001
▴ 40
0
votes
0
replies
47
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
updated 5 hours ago by
Ram
43k • written 7 hours ago by
Guille
• 0
0
votes
0
replies
53
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 8 hours ago by
Ram
43k • written 9 hours ago by
vanbelj
▴ 40
0
votes
0
replies
51
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 7 hours ago by
GenoMax
141k • written 10 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 10 hours ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
2
votes
2
replies
189
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 13 hours ago by
dsull
★ 5.8k • written 20 hours ago by
Aaliya
▴ 10
3
votes
0
replies
95
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 4 hours ago by
Ram
43k • written 15 hours ago by
Claire Watson
▴ 60
0
votes
2
replies
165
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 4 hours ago by
Ram
43k • written 1 day ago by
The_PyPanda
▴ 10
0
votes
0
replies
94
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
16 hours ago by
HarperReed
• 0
3
votes
3
replies
167
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 13 hours ago by
GenoMax
141k • written 16 hours ago by
sapuizait
▴ 10
1
vote
0
replies
66
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
18 hours ago by
KABILAN
▴ 50
0
votes
0
replies
67
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 4 hours ago by
Ram
43k • written 18 hours ago by
SineWave
• 0
0
votes
0
replies
68
views
RNA-seq: full length gene
RNA-seq
updated 8 hours ago by
Ram
43k • written 19 hours ago by
Nargis
• 0
0
votes
1
reply
96
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 20 hours ago by
Jeremy Leipzig
22k • written 21 hours ago by
zihanss
• 0
0
votes
0
replies
64
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
21 hours ago by
turcoa1
• 0
3
votes
3
replies
196
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 1 day ago by
swbarnes2
14k • written 1 day ago by
M
• 0
0
votes
0
replies
78
views
Designing single-stable RNA molecules
structure
RNA
1 day ago by
Edna
• 0
0
votes
0
replies
90
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
1 day ago by
simplitia
▴ 130
0
votes
1
reply
127
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
183
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
215
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 1 day ago by
Ram
43k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
149
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
259
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 10 hours ago by
bk11
★ 2.4k • written 1 day ago by
starswillfade
▴ 10
0
votes
0
replies
91
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
86
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
80
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
1 day ago by
Emily
▴ 10
1
vote
0
replies
100
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
85
views
how to read graph_test output of monocle 3
monocle3
1 day ago by
synat.keam
▴ 100
0
votes
0
replies
115
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
1 day ago by
Assaf
• 0
0
votes
1
reply
416
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
246
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
1 day ago by
QX
• 0
2
votes
1
reply
169
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
98
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
1 day ago by
Aspire
▴ 300
2
votes
4
replies
248
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
212
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
149
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
211
views
Highest variable features in single cell data
single-cell
updated 4 hours ago by
bk11
★ 2.4k • written 1 day ago by
Kazo
• 0
0
votes
1
reply
181
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
235
views
PCA plot
DESeq2
PCAplot
updated 16 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
2
votes
3
replies
274
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 5 hours 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
120
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
2 days ago by
4fzcgueyp5
• 0
116,627 results • Page
1 of 2333
Recent Votes
Comment: Heatmap and rna-seq
Answer: Heatmap and rna-seq
Comment: Heatmap and rna-seq
A: should FASTA files be sorted before indexed with SAMtools?
Answer: A faidx-indexed FASTA format file or a FASTA format file
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
Comment: Create a new bed file with all pairwise combinations between two other bed files
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Answer: How to use limma to find differentially expressed genes in response to a continu
by
Gordon Smyth
★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing
by
cao510927
▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
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…
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