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116,624 results • Page
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Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 1 hour ago by
ATpoint
82k • written 1 hour ago by
chaco001
▴ 40
0
votes
0
replies
18
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
updated 30 minutes ago by
Ram
43k • written 1 hour ago by
Guille
• 0
0
votes
0
replies
38
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 3 hours ago by
Ram
43k • written 4 hours ago by
vanbelj
▴ 40
0
votes
0
replies
39
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 2 hours ago by
GenoMax
141k • written 4 hours ago by
hagl
▴ 10
0
votes
4
replies
358
views
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 5 hours ago by
pinheirofabiano
▴ 10 • written 3 days ago by
qudrat.nii
▴ 10
0
votes
5
replies
266
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 3 hours ago by
Pierre Lindenbaum
161k • written 14 hours ago by
J
• 0
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 5 hours ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
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
2
votes
2
replies
173
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 8 hours ago by
dsull
★ 5.8k • written 14 hours ago by
Aaliya
▴ 10
3
votes
0
replies
82
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
scRNA
Machinelearning
GenerativeAI
9 hours ago by
Claire Watson
▴ 60
0
votes
2
replies
153
views
Rare Disease Variant Pathway Analysis
Pathway
analysis
10 hours ago by
The_PyPanda
▴ 10
0
votes
0
replies
78
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
10 hours ago by
HarperReed
• 0
3
votes
3
replies
143
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 8 hours ago by
GenoMax
141k • written 11 hours ago by
sapuizait
▴ 10
1
vote
0
replies
55
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
13 hours ago by
KABILAN
▴ 50
0
votes
0
replies
55
views
Running Phylogenetic Analysis With NCBI Genome
population
genetics
phylogenetic
species
sequencing
13 hours ago by
SineWave
• 0
0
votes
0
replies
57
views
RNA-seq: full length gene
RNA-seq
updated 3 hours ago by
Ram
43k • written 13 hours ago by
Nargis
• 0
0
votes
1
reply
84
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 15 hours ago by
Jeremy Leipzig
22k • written 15 hours ago by
zihanss
• 0
0
votes
0
replies
53
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
15 hours ago by
turcoa1
• 0
3
votes
3
replies
182
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 22 hours ago by
swbarnes2
14k • written 1 day ago by
M
• 0
0
votes
0
replies
68
views
Designing single-stable RNA molecules
structure
RNA
22 hours ago by
Edna
• 0
0
votes
0
replies
80
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
22 hours ago by
simplitia
▴ 130
0
votes
1
reply
119
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 23 hours ago by
ATpoint
82k • written 1 day ago by
AaronJaime
• 0
0
votes
2
replies
173
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
202
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 22 hours ago by
Ram
43k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
139
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
updated 23 hours ago by
Ram
43k • written 1 day ago by
Francesco
▴ 10
1
vote
5
replies
236
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 4 hours ago by
bk11
★ 2.4k • written 1 day ago by
starswillfade
▴ 10
0
votes
0
replies
82
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
78
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 23 hours ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
72
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
1 day ago by
Emily
▴ 10
1
vote
0
replies
90
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
76
views
how to read graph_test output of monocle 3
monocle3
1 day ago by
synat.keam
▴ 100
0
votes
0
replies
104
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
1 day ago by
Assaf
• 0
0
votes
1
reply
408
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
238
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
1 day ago by
QX
• 0
2
votes
1
reply
161
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
89
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
1 day ago by
Aspire
▴ 300
2
votes
4
replies
239
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
updated 23 hours ago by
Ram
43k • written 1 day ago by
ashaneev07
▴ 20
2
votes
3
replies
204
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
141
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
2
replies
170
views
Highest variable features in single cell data
single-cell
updated 23 hours ago by
Ram
43k • written 1 day ago by
Kazo
• 0
0
votes
1
reply
171
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
218
views
PCA plot
DESeq2
PCAplot
updated 10 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
2
votes
3
replies
205
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 20 minutes 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
113
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
292
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
221
views
Annovar using R package
Annovar
gnomAD
R
23 hours ago by
DKA
▴ 40
0
votes
2
replies
204
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
8
votes
8
replies
536
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 1 day ago by
swbarnes2
14k • written 2 days ago by
Aaliya
▴ 10
116,624 results • Page
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Comment: PCA plot
C: RNA seq library size
RNA seq library size
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
Comment: Convert SAM to BAM
Comment: Should I use unpaired reads from trimmomatic
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Recent Replies
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?
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%d\…
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…
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