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
122,011 results • Page
288 of 2441
Sort: Rank
Rank
Views
Votes
Replies
0
votes
4
replies
1.6k
views
Between sample normalization without replicates
normalization
RNA-Seq
2.6 years ago by
GR
▴ 400
0
votes
2
replies
1.2k
views
If using singeR return more clusters than available ones should I do reclustering?
singleR
updated 2.6 years ago by
jared.andrews07
★ 19k • written 2.6 years ago by
paria
▴ 110
2
votes
3
replies
1.9k
views
Sample Level Filtering During GATK Germline Short Variant Discovery
Genotyping
genomics
vcf
GATK
germline
2.6 years ago by
jon.klonowski
▴ 210
1
vote
3
replies
1.0k
views
How/when to merge biological replicates during GATK work flow
RNA-Editing
GATK
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
Genetics
▴ 30
0
votes
1
reply
1.4k
views
allele frequency from vcf
SNP
genome
updated 2.6 years ago by
AMARU
• 0 • written 4.6 years ago by
niyomiw88
• 0
2
votes
6
replies
1.8k
views
Genes in 10x don't match genes in ENSBL
gene_mapping
bioconductor
singleCellRNAseq
updated 2.6 years ago by
jv
★ 1.9k • written 2.6 years ago by
Sandra
▴ 10
4
votes
1
reply
1.4k
views
Forum:
Open problems in genomics 2023
genomics
pangenomics
updated 2.6 years ago by
GenoMax
154k • written 2.6 years ago by
colindaven
8.0k
0
votes
8
replies
2.7k
views
GATK4.3 ApplyBQSR
ApplyBQSR
2.6 years ago by
wonde2000
• 0
2
votes
5
replies
1.7k
views
How many refseqs are in refseq.genomes.k21.s1000.msh?
mash
refseq
2.6 years ago by
SushiRoll
▴ 140
3
votes
3
replies
3.4k
views
how to use make.names commnad in r while using rbind function
R
2.6 years ago by
rheab1230
▴ 150
7
votes
5
replies
1.9k
views
kallisto -s o error
kallisto
RNA-seq
2.6 years ago by
1_GOld
• 0
0
votes
2
replies
1.0k
views
change the axis scale in mds plot
r
2.6 years ago by
Chironex
▴ 50
1
vote
4
replies
2.4k
views
Uniprot id to GO terms
UniProt
GO
updated 2.6 years ago by
Elisabeth Gasteiger
★ 2.4k • written 2.6 years ago by
Shweta
• 0
0
votes
0
replies
501
views
Identifying tagging variants / haplotypes in GWAS data
SNPs
GWAS
LD
haplotypes
plink
2.6 years ago by
Christopher
• 0
6
votes
4
replies
4.0k
views
10X V3 library with only one fastq file
scRNA-seq
V3
SRA
kallisto
10X
2.6 years ago by
Julien
▴ 10
3
votes
4
replies
3.2k
views
How to convert PHYLIP to NEWICK format (pairwise distance matrix)
python
phylogeny
updated 2.6 years ago by
Joe
22k • written 2.6 years ago by
Linda
• 0
3
votes
3
replies
1.7k
views
Error while converting GFF file to GTF using AGAT
GFF3
GTF
AGAT
updated 2.6 years ago by
Juke34
9.3k • written 2.6 years ago by
Genetics
▴ 30
2
votes
3
replies
1.8k
views
reference for freebayes or samtools mpileup after extracting chromosome from alignment
samtools
SNP
alignment
freebayes
updated 2.3 years ago by
Ram
45k • written 2.6 years ago by
poecile.pal
▴ 50
0
votes
2
replies
961
views
Integrating single-nucleus RNA-seq and single-cell RNA-seq datasets
snRNAseq
single-cell
scRNAseq
2.6 years ago by
bompipi95
▴ 170
7
votes
4
replies
2.4k
views
Nextflow workflow errors when run from Scratch dir?
bwa
nextflow
2.6 years ago by
Eliveri
▴ 350
2
votes
1
reply
1.1k
views
Why does deepvariant make a call if the allele does not exist in the sample?
genome
variant-calling
genetics
genotype
deepvariant
updated 24 months ago by
Ram
45k • written 2.6 years ago by
Frieda
▴ 60
1
vote
3
replies
2.0k
views
Getting unspliced counts for scRNA-seq data generated from cellranger aggr pipeline
cellranger
loom
scVelo
scRNA
aggr
updated 2.6 years ago by
fracarb8
★ 1.7k • written 2.6 years ago by
Luna_P
▴ 20
5
votes
8
replies
4.5k
views
How exactly can I define promoter region from GENCODE annotation GTF file?
promoter
protein-coding
GENCODE
annotation
2.6 years ago by
ConvolutedGenome
▴ 60
0
votes
2
replies
881
views
Knownsite vcf file not available.
KnownSites
recalibration
VCF
GATK
updated 2.3 years ago by
Ram
45k • written 2.6 years ago by
Genetics
▴ 30
0
votes
0
replies
723
views
Filtering mapping results by percent identity and aligned percent?
sam
bowtie2
minimap2
mapping
bwa
2.6 years ago by
kmat
• 0
1
vote
2
replies
1.2k
views
how to iteratively search sequences against sequence database using profile HMM
protein
pHMM
2.6 years ago by
zhangdengwei
▴ 210
0
votes
0
replies
462
views
Is there a array-based population dataset with phenotypes like eye colour available?
gwas
2.6 years ago by
optimistsso4co3
▴ 140
1
vote
4
replies
2.5k
views
Data Imputation for performing UMAP
R
Imputation
UMAP
2.6 years ago by
jscl1n22
• 0
6
votes
3
replies
1.9k
views
How to make line graph with circles in R
R
updated 2.6 years ago by
Chirag Parsania
★ 2.0k • written 2.6 years ago by
cthangav
▴ 110
0
votes
0
replies
468
views
extract 1D features (genes) from 2D dataset (TADs)
hic
tads
genes
2.6 years ago by
J.
• 0
2
votes
2
replies
1.1k
views
how best to analyze vcf files
vcf
updated 2.6 years ago by
iraun
6.2k • written 2.6 years ago by
Mali
• 0
0
votes
0
replies
660
views
News:
Environmental Metagenomics course
Environmental-Metagenomics
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
Physalia-courses
★ 2.6k
0
votes
4
replies
1.7k
views
what does total count mean at a location in IGV
bam
samtools
igv
2.6 years ago by
newDarkAB09834
▴ 20
1
vote
2
replies
1.1k
views
New to RNA Seq Analysis ...
RNA-Seq
updated 2.6 years ago by
matthew.pace
▴ 60 • written 2.6 years ago by
sinha.shriprakash
▴ 20
0
votes
0
replies
573
views
snpeff annotation query
snpeff
structural-variation
VCF
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
prasundutta87
▴ 730
0
votes
1
reply
828
views
SNP data - significance heterozygosity test?
significance-test
SNP
updated 2.6 years ago by
Ram
45k • written 2.7 years ago by
Roland
▴ 20
7
votes
5
replies
2.5k
views
Nextflow: [E::bwa_idx_load_from_disk] fail to locate the index files
sge
bwa
nextflow
2.6 years ago by
Eliveri
▴ 350
0
votes
0
replies
815
views
Clade model C of PAML to detect positive selection in coding nucleotide sequences
selection
evolution
PAML
CDS
2.6 years ago by
Denis
▴ 320
0
votes
0
replies
517
views
Filtering genes study-specific before Harmony integration?
Harmony
iNTEGRATION
scRNAseq
2.6 years ago by
ralbero
▴ 10
0
votes
10
replies
3.0k
views
6 follow
BLAST Database error: No alias or index file found for nucleotide database
alignment
updated 2.6 years ago by
gernophil
▴ 130 • written 4.9 years ago by
czb321
• 0
5
votes
3
replies
1.7k
views
Forum:
Someone posted the same question to StackOverflow and Biostars. The results will blow your mind.
meta
updated 2.6 years ago by
Joe
22k • written 2.6 years ago by
Cornelius
▴ 80
5
votes
6
replies
1.9k
views
Trimmomatic generated two (reverse-forward) paired-files with different number of reads
Trimmomatic
RNA-Seq
2.6 years ago by
Pegasus
▴ 130
0
votes
1
reply
1.4k
views
Pangenome: Gene presence and absence analysis
sequencing
pangenome
updated 2.6 years ago by
colindaven
8.0k • written 6.1 years ago by
ysas
▴ 10
1
vote
2
replies
1.7k
views
Check my understanding - difference between number of reads sequenced and Seurat nCount_RNA
scRNAseq
2.6 years ago by
bompipi95
▴ 170
3
votes
2
replies
1.3k
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
PAAD
KM
Plot
TCGA
2.6 years ago by
Manav
• 0
3
votes
3
replies
1.6k
views
Filtering of tricky overlapping sites in VCF
vcf
bcftools
2.6 years ago by
cfos4698
★ 1.2k
0
votes
3
replies
1.3k
views
Summarizing permutation test/ bootstrap result for multiple samples for single-cell RNAseq data
single-cell
RNA-seq
2.6 years ago by
cwwong13
▴ 40
0
votes
6
replies
3.2k
views
Getting matrix of QDs from VCF file
vcf
snp
updated 2.6 years ago by
wlei091226
• 0 • written 9.0 years ago by
Jautis
▴ 580
6
votes
3
replies
1.8k
views
How to extract FASTA headers in R
r
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
WUSCHEL
▴ 860
2
votes
2
replies
1.5k
views
Z-score difference between Z group means
Statistics
differential-expression
updated 2.6 years ago by
LChart
5.1k • written 2.6 years ago by
schulpen_91
▴ 30
122,011 results • Page
288 of 2441
Recent Votes
Analysis of Smart-Seq3 data with kallisto-bustools
Answer: Tools/pipeline for analysis of smart-seq3 data
Answer: Tools/pipeline for analysis of smart-seq3 data
Comment: DESeq2 on metagenome KO counts
Comment: GUI commercial software for 10x single cell gene expression analysis
Comment: GUI commercial software for 10x single cell gene expression analysis
Comment: Pseudogene - scarce info
Recent Locations •
All
Bologna,
2 minutes ago
London, UK,
7 minutes ago
United States,
12 minutes ago
Australia,
16 minutes ago
Machhagan,
48 minutes ago
China,Xi'an,
48 minutes ago
Whitefish, MT,
49 minutes ago
Recent Awards •
All
Popular Question
to
wdpang
• 0
Popular Question
to
MolGeek
▴ 80
Popular Question
to
Andrzej Zielezinski
11k
Teacher
to
andres.firrincieli
3.9k
Teacher
to
Aleksandra
▴ 180
Popular Question
to
vernonlim98
• 0
Teacher
to
GenoMax
154k
Recent Replies
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine
by
Ram
45k
Do you have a plan to make an English version of the UI?
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine
by
Edward
• 0
This can visualize the parameters of the generated workflow, software, and scripts, and manage the docker process of the script, software, …
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine
by
ATpoint
89k
Can you summarize in one sentence what the use case is? Is this a workflow manager?
Comment: Pseudogene - scarce info
by
ATpoint
89k
This reminds me strongly on my "masters" courses (doesn't deserve that name tbf). "Here is some poorly-described project with little to no …
Answer: scVI vs Harmony, which is better for cell type based clustering in brain tissue?
by
ATpoint
89k
There is no "better" is my experience. It always depends on the dataset. Try both and integrate your biological knowledge to decide which m…
Comment: DESeq2 on metagenome KO counts
by
Aleksandra
▴ 180
I just wrote that I misunderstood your initial question.
Comment: DESeq2 on metagenome KO counts
by
Aleksandra
▴ 180
What exactly did I not get?
Comment: Interpreting genomic features distribution for CUT&RUN peaks
by
rfran010
★ 1.7k
If I understand correctly, you see increased signal at TSS sites compared to control (taller peaks in browser). However, 92% of the 450 siS…
Comment: combine VCF from diploid reference/haplotypes for the same sample
by
cmdcolin
★ 4.3k
this question is a little similar to your previous question (https://www.biostars.org/p/9614638/). just as added info, here is a tool calle…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space?
by
aj123
▴ 130
As mentioned above, I just got the raw fastq files from the ftp site listed.
Comment: DESeq2 on metagenome KO counts
by
ATpoint
89k
This statement makes zero sense in response to what I wrote.
Comment: DESeq2 on metagenome KO counts
by
Aleksandra
▴ 180
I focused on the fact that DESeq2 models overdispersion, but overlooked its implicit assumption: normalisation works when the main source o…
Comment: DESeq2 on metagenome KO counts
by
Aleksandra
▴ 180
Thank you very much. I mistakenly drew a superficial analogy. I equated KO counters with gene counters.
Comment: DESeq2 on metagenome KO counts
by
ATpoint
89k
Both vst or logcpm will favor expression level (magnitude of counts) rather than differences in a hclust/heatmap. For differences you need …
Comment: DESeq2 on metagenome KO counts
by
ATpoint
89k
The DESeq2 developer has advised many times against DESeq2 for metagenomics. Please search for related posts over at support.bioconductor.o…
Traffic: 3759 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