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116,635 results • Page
1 of 2333
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0
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6
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Downloading full alignments from Pfam
pfam
10 minutes ago by
bef1
• 0
0
votes
1
reply
636
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 19 minutes ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
1
vote
1
reply
144
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 4 hours ago by
ATpoint
82k • written 1 day ago by
vanbelj
▴ 40
2
votes
6
replies
1.1k
views
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 3 hours ago by
Ram
43k • written 8 months ago by
Calum
▴ 10
0
votes
0
replies
36
views
adjusting for confounders in LMER in R
confounders
LMER
R
4 hours ago by
rene.j.erhardt
▴ 20
0
votes
2
replies
114
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
updated 6 hours ago by
Ram
43k • written 8 hours ago by
Ruqaiya
• 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
1
reply
102
views
How to assign cell types after integration in scRNA
integration
conditions
ScRNA
seq
updated 4 hours ago by
ATpoint
82k • written 14 hours ago by
Francesco
▴ 10
0
votes
0
replies
69
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
14 hours ago by
tnminh89
▴ 10
7
votes
7
replies
549
views
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
7 hours ago by
noodle
▴ 520
0
votes
0
replies
72
views
Extract protein sequence
fasta
alighment
blast
15 hours ago by
anna
▴ 20
0
votes
0
replies
69
views
Filter low express genes in microarray data
microarray
16 hours ago by
Chris
▴ 260
0
votes
1
reply
258
views
absolute path for symbolic links in Snakefile
Snakemake
updated 16 hours ago by
Jesse
▴ 740 • written 8 days ago by
yifangt86
▴ 60
0
votes
2
replies
265
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 16 hours ago by
Jesse
▴ 740 • written 3 days ago by
Broccoli
• 0
2
votes
3
replies
247
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 17 hours ago by
Arup Ghosh
3.2k • written 1 day ago by
chaco001
▴ 40
1
vote
3
replies
250
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
updated 10 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
O.rka
▴ 710
0
votes
1
reply
157
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 1 day ago by
Gordon Smyth
★ 7.0k • written 1 day ago by
hagl
▴ 10
0
votes
2
replies
191
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
1 day ago by
Guille
• 0
1
vote
1
reply
143
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
updated 1 day ago by
Gordon Smyth
★ 7.0k • written 1 day ago by
pairedttest
▴ 10
3
votes
6
replies
1.9k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 1 day ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
0
votes
0
replies
338
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
1 day ago by
biocellbio
• 0
4
votes
8
replies
527
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 1 day ago by
Alex Reynolds
35k • written 2 days ago by
J
▴ 10
4
votes
7
replies
582
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 1 day ago by
dsull
★ 5.9k • written 5 days ago by
qudrat.nii
▴ 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 1 day ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
2
votes
2
replies
256
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 2 days ago by
dsull
★ 5.9k • written 2 days ago by
Aaliya
▴ 10
3
votes
0
replies
149
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 1 day ago by
Ram
43k • written 2 days ago by
Claire Watson
▴ 60
0
votes
2
replies
220
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 1 day ago by
Ram
43k • written 2 days ago by
The_PyPanda
▴ 10
0
votes
0
replies
154
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
2 days ago by
HarperReed
• 0
3
votes
3
replies
225
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 1 day ago by
GenoMax
141k • written 2 days ago by
sapuizait
▴ 10
1
vote
0
replies
116
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
2 days ago by
KABILAN
▴ 50
0
votes
0
replies
126
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 1 day ago by
Ram
43k • written 2 days ago by
SineWave
• 0
0
votes
0
replies
121
views
RNA-seq: full length gene
RNA-seq
updated 1 day ago by
Ram
43k • written 2 days ago by
Nargis
• 0
1
vote
7
replies
335
views
gvcf joint calling
WES
GATK
VCF
gVCF
3 hours ago by
zihanss
• 0
0
votes
0
replies
114
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
2 days ago by
turcoa1
• 0
3
votes
3
replies
244
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 2 days ago by
swbarnes2
14k • written 2 days ago by
M
• 0
0
votes
0
replies
125
views
Designing single-stable RNA molecules
structure
RNA
2 days ago by
Edna
• 0
0
votes
0
replies
139
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
2 days ago by
simplitia
▴ 130
0
votes
1
reply
176
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 2 days ago by
ATpoint
82k • written 2 days ago by
AaronJaime
• 0
0
votes
2
replies
237
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 2 days ago by
GenoMax
141k • written 3 days ago by
Begonia_pavonina
▴ 150
0
votes
2
replies
269
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 2 days ago by
Ram
43k • written 3 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
2
replies
261
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
14 hours ago by
Francesco
▴ 10
1
vote
6
replies
374
views
ScRNA data question
scRNA
Vlnplot
Samples
1 day ago by
starswillfade
▴ 10
0
votes
0
replies
141
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
2 days ago by
avocado123
• 0
0
votes
0
replies
133
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
132
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
2 days ago by
Emily
▴ 10
1
vote
0
replies
149
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
2 days ago by
rohitsatyam102
▴ 850
0
votes
0
replies
132
views
how to read graph_test output of monocle 3
monocle3
2 days ago by
synat.keam
▴ 100
0
votes
0
replies
163
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
2 days ago by
Assaf
• 0
0
votes
1
reply
462
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 2 days ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
3
votes
4
replies
305
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
2 days ago by
QX
• 0
116,635 results • Page
1 of 2333
Recent Votes
Answer: ChIP-seq datasets: input samples omitted?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
A: Deeptools plotHeatmap - Maintain Order of Input BED file
Comment: NGS forensics: how to know if data is fabricated
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Answer: DNA methylation preprocessing
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Recent Replies
Answer: Can I run cellassign on samples independently if there is batch effect present?
by
Francesco
▴ 10
Hi! Whenever you do make independent analysis or aggregate data and analyze them, most cell type assignment tools start from raw counts to …
Comment: gvcf joint calling
by
zihanss
• 0
Thanks for your comment, I get it now.
Answer: ChIP-seq datasets: input samples omitted?
by
ATpoint
82k
In my hands (and from what I know based on many years here) inputs are almost exclusively used during peak calling to correct for loci-spec…
Comment: How to assign cell types after integration in scRNA
by
ATpoint
82k
No difference here. After all you typically want a label per cluster/group, so either subset to the control condition to do the assignment,…
Comment: Differential Expression using Isoseq-supplemented reference transcriptome
by
gaoanwei
• 0
I found the question and ASK the GPT4 turbo
Answer: Differential Expression using Isoseq-supplemented reference transcriptome
by
gaoanwei
• 0
Your approach seems reasonable and well-informed, though it's perhaps less customary in the field, which could be why you haven't found pap…
Answer: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
It takes 29 seconds to assemble this genome (20 CPUs) with the following statistics: 135 contigs, total 2821177 bp, min 200 bp, max …
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
IMO (and unfortunately) there needs to be an effort to develop these algorithms.
Comment: gvcf joint calling
by
Jeremy Leipzig
22k
the samples that are `./.` have no coverage (or not enough to call a genotype) and the `0/0` are homozygous reference
Answer: How many reads for WGS Sequencing?
by
GenoMax
141k
Did you download the complete dataset available from ENA/NCBI SRA? This is an older dataset (from 2012) with a total of 1146212 reads and 1…
Comment: When to use .vcf or .gvcf files from GATK HaplotypeCaller?
by
zihanss
• 0
Hello, I want to know that why my gVCF files have "./." besides "0/0", "1/1"? Thanks
Comment: gvcf joint calling
by
zihanss
• 0
![enter image description here][1] [1]: /media/images/15eedc1a-b2c6-4966-be39-b5173dab And I confused with the file that has "./." and…
Comment: gvcf joint calling
by
zihanss
• 0
![enter image description here][1] [1]: /media/images/16fd502c-4e01-4f56-8562-0e0d4aac Okay, this is the merged gVCF file.
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
Mensur Dlakic
★ 27k
Enzymes under the umbrella of `1.1.1.-` work `with NAD(+) or NADP(+) as acceptor`. That only tells you about their cofactors, but not about…
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I don't think people have undertaken the effort to create an anomaly detector for RNAseq -- people's efforts are dedicated towards developi…
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