Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : all time
all time
today
this week
this month
this year
116,620 results • Page
1 of 2333
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
1
view
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
just now by
hagl
▴ 10
0
votes
4
replies
318
views
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 34 minutes ago by
pinheirofabiano
▴ 10 • written 3 days ago by
qudrat.nii
▴ 10
0
votes
5
replies
202
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 45 minutes ago by
Pierre Lindenbaum
161k • written 10 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 10 minutes ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
2
votes
2
replies
140
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 3 hours ago by
dsull
★ 5.8k • written 9 hours ago by
Aaliya
▴ 10
2
votes
0
replies
61
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
0
votes
2
replies
139
views
Rare Disease Variant Pathway Analysis
Pathway
analysis
5 hours ago by
The_PyPanda
▴ 10
0
votes
0
replies
63
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
5 hours ago by
HarperReed
• 0
795
votes
167
replies
141k
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
2
replies
87
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 3 hours ago by
GenoMax
141k • written 6 hours ago by
sapuizait
▴ 10
1
vote
0
replies
47
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
8 hours ago by
KABILAN
▴ 50
0
votes
0
replies
46
views
Running Phylogenetic Analysis With NCBI Genome
population
genetics
phylogenetic
species
sequencing
8 hours ago by
SineWave
• 0
0
votes
0
replies
45
views
RNA-seq: full length gene
identification
gene
full
length
8 hours ago by
Nargis
• 0
0
votes
1
reply
74
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 10 hours ago by
Jeremy Leipzig
22k • written 10 hours ago by
zihanss
• 0
0
votes
0
replies
42
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
10 hours ago by
turcoa1
• 0
3
votes
3
replies
173
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 16 hours ago by
swbarnes2
14k • written 23 hours ago by
M
• 0
0
votes
0
replies
61
views
Designing single-stable RNA molecules
structure
RNA
17 hours ago by
Edna
• 0
0
votes
0
replies
70
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
17 hours ago by
simplitia
▴ 130
0
votes
1
reply
108
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 18 hours ago by
ATpoint
82k • written 19 hours ago by
AaronJaime
• 0
0
votes
2
replies
167
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 20 hours ago by
GenoMax
141k • written 1 day ago by
Begonia_pavonina
▴ 150
0
votes
2
replies
192
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 16 hours ago by
Ram
43k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
131
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
updated 18 hours ago by
Ram
43k • written 1 day ago by
Francesco
▴ 10
1
vote
5
replies
188
views
ScRNA data question
scRNA
Vlnplot
Samples
updated just now by
bk11
★ 2.4k • written 1 day ago by
starswillfade
▴ 10
0
votes
0
replies
75
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
71
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 18 hours ago by
Ram
43k • written 21 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
65
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
21 hours ago by
Emily
▴ 10
1
vote
0
replies
82
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
22 hours ago by
rohitsatyam102
▴ 850
0
votes
0
replies
68
views
how to read graph_test output of monocle 3
monocle3
22 hours ago by
synat.keam
▴ 100
0
votes
0
replies
94
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
22 hours ago by
Assaf
• 0
0
votes
1
reply
398
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 23 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
3
votes
4
replies
229
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
19 hours ago by
QX
• 0
2
votes
1
reply
155
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 1 day ago by
Adrian Altenhoff
★ 1.1k • written 1 day ago by
hemantcnaik
• 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
2
votes
4
replies
231
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
updated 18 hours ago by
Ram
43k • written 1 day ago by
ashaneev07
▴ 20
2
votes
3
replies
195
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
134
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
164
views
Highest variable features in single cell data
single-cell
updated 18 hours ago by
Ram
43k • written 1 day ago by
Kazo
• 0
0
votes
1
reply
163
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
2.3k
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
0
votes
2
replies
199
views
PCA plot
DESeq2
PCAplot
updated 5 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
0
votes
1
reply
164
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 18 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
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
2
votes
3
replies
285
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 3 days ago by
Mensur Dlakic
★ 27k • written 4 days ago by
emmanouil.a
▴ 120
0
votes
2
replies
213
views
Annovar using R package
Annovar
gnomAD
R
18 hours ago by
DKA
▴ 40
0
votes
2
replies
196
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
biochugs
• 0
8
votes
8
replies
518
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 1 day ago by
swbarnes2
14k • written 2 days ago by
Aaliya
▴ 10
1
vote
8
replies
766
views
Adding CB tag to bam file
samtools
bam
updated 1 day ago by
Pierre Lindenbaum
161k • written 7 days ago by
Maria
• 0
1
vote
10
replies
908
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
1 day ago by
DKA
▴ 40
0
votes
2
replies
797
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 1 day ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
116,620 results • Page
1 of 2333
Recent Votes
Answer: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: Is there a software that can compare phylogenetic trees to each othe (face to fa
Comment: Is there a software that can compare phylogenetic trees to each othe (face to fa
Recent Locations •
All
Canada,
just now
United States,
just now
United States,
1 minute ago
Italy,
2 minutes ago
France/Nantes/Institut du Thorax - INSERM UMR1087,
3 minutes ago
Canada,
4 minutes ago
Turkey,
5 minutes ago
Recent Awards •
All
Scholar
to
bk11
★ 2.4k
Popular Question
to
vinayjrao
▴ 250
Supporter
to
Jalil Sharif
▴ 80
Popular Question
to
sil_bioinfo
▴ 40
Popular Question
to
sapuizait
▴ 10
Voter
to
analyst
▴ 30
Scholar
to
ATpoint
82k
Recent Replies
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…
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…
Traffic: 3290 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6