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122,011 results • Page
606 of 2441
Sort: Rank
Rank
Views
Votes
Replies
6
votes
4
replies
6.7k
views
Pandas dataframe to H5ad file
H5
python
pandas
4.2 years ago by
roy.granit
▴ 890
0
votes
3
replies
1.8k
views
Missing mappability file for mm10
mm10
mappability
updated 4.2 years ago by
Ram
45k • written 6.3 years ago by
fabbri.marco
▴ 20
0
votes
1
reply
2.7k
views
Clusterprofiler object 'GO2ONT' not found
get_GO_data
go2ont
enrichgo
clusterprofiler
GO
4.2 years ago by
corinne_hutfilz
• 0
0
votes
3
replies
1.5k
views
CreatePHG_step2_consensu
PHGwiki
PHG
updated 4.2 years ago by
pjb39
▴ 220 • written 4.2 years ago by
bp
• 0
0
votes
0
replies
409
views
Can´t create a consensus file from my VCF and reference genome
migrate-n
4.2 years ago by
Dieggar
• 0
1
vote
4
replies
2.2k
views
R package for filtering expression data
gene-expression
r
EMA
updated 4.2 years ago by
Ram
45k • written 4.2 years ago by
melissachua90
▴ 70
0
votes
1
reply
1.0k
views
ARACNE Minet R studio
ARACNE
Minet
updated 4.2 years ago by
andres.firrincieli
3.9k • written 4.2 years ago by
ashtay
• 0
0
votes
2
replies
1.0k
views
Should I run GISTIC2.0 for cases/controls separately?
GISTIC2.0
CNV
CNA
updated 4.2 years ago by
Ram
45k • written 4.2 years ago by
@e95917ed
• 0
0
votes
1
reply
612
views
Problem for interpreting results of ClusterViz
Cytoscape
updated 4.2 years ago by
Scooter
▴ 310 • written 4.2 years ago by
fahim
▴ 20
0
votes
1
reply
784
views
Cytoscape - How to filter when starting from a complete network, built from a gene-to-gene adjacency matrix
cytoscape
updated 4.2 years ago by
Scooter
▴ 310 • written 4.2 years ago by
JP
▴ 30
0
votes
1
reply
613
views
Cytoscape: GeneMANIA plug-in output.
GeneMANIA
analysis
cytoscape
network
analysis.
updated 4.2 years ago by
Scooter
▴ 310 • written 4.2 years ago by
robynadams
• 0
2
votes
2
replies
1.3k
views
How to use RINalyzer plugin in cytoscape
cytoscape
RINalyzer
networks
updated 4.2 years ago by
Scooter
▴ 310 • written 4.3 years ago by
rohitsatyam102
▴ 940
2
votes
3
replies
2.0k
views
How to plot/combine biological replicates on a genomic features plot for methylated array?
array
methylation
beadchip
plot
features
genomic
updated 4.2 years ago by
Papyrus
★ 3.1k • written 4.2 years ago by
Pratik
★ 1.1k
10
votes
8
replies
8.1k
views
Bcftools how to add DP to FORMAT field (get per sample read depth for REF vs ALT alleles )
bcftools
snp
vcf
calling
updated 4.1 years ago by
Michal Nevo
▴ 140 • written 4.2 years ago by
Linda
▴ 80
11
votes
13
replies
4.0k
views
Why is WGS/WES depth of Y chromosome highly variable?
chromosome-Y
whole-genome-sequencing
updated 2.8 years ago by
Ram
45k • written 4.2 years ago by
samuelandjw
▴ 270
3
votes
7
replies
2.7k
views
How to infer segment direction from vcf
SV
vcf
NGS
4.2 years ago by
octpus616
▴ 120
0
votes
0
replies
1.2k
views
Explanation of generatio from clusterProfiler package
transcriptomic
proteomics
4.2 years ago by
javanokendo
▴ 60
2
votes
5
replies
2.6k
views
Reference file for base recalibration
base
NGS
recalibration
preprocessing
GATK
4.2 years ago by
priya.bmg
▴ 70
5
votes
2
replies
2.6k
views
Calculating minor allele frequency for GnomAD VCF file
gnomAD
genome
updated 4.2 years ago by
Kalin
▴ 50 • written 4.9 years ago by
Jamie Watson
▴ 20
8
votes
5
replies
5.7k
views
Quickly get allele frequencies from Gnomad
gnomad
allele freq
ngs
updated 3.0 years ago by
Kalin
▴ 50 • written 5.2 years ago by
Floydian_slip
▴ 170
4
votes
10
replies
3.5k
views
Help With TCGAbiolinks package
rnaseq
TCGA
tcgabiolinks
R
bioconductor
4.2 years ago by
daniela.paola.s.p
▴ 70
0
votes
4
replies
1.9k
views
How to convert gene names to EC numbers?
database
updated 4.2 years ago by
lieven.sterck
16k • written 4.2 years ago by
dpc
▴ 250
4
votes
3
replies
2.4k
views
RNA-Seq Mapping Genome or Transcriptome
Genome
Transcriptome
Rna-Seq
updated 4.2 years ago by
bigomics.team
▴ 90 • written 4.2 years ago by
santos48
▴ 40
1
vote
0
replies
833
views
Tool:
Omics Playground: visualization and analysis of transcriptomics and proteomics data
proteomics
RNA
RNA-seq
scRNA-seq
omics
data
4.2 years ago by
bigomics.team
▴ 90
0
votes
0
replies
626
views
Biotype assignment for co-expression network
biotype
co-expression
4.2 years ago by
imaparna27
▴ 20
2
votes
5
replies
4.3k
views
collapsing pacbio reads into a single sequence
pacbio
4.2 years ago by
Sara
▴ 280
0
votes
0
replies
927
views
News:
Online training -Metabolomics in R
Metabolomics
4.2 years ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
1.0k
views
Older version of markers from Chocophlan
Chocophlan
Metaphlan
updated 4.2 years ago by
Ram
45k • written 4.2 years ago by
fyfes
▴ 70
2
votes
2
replies
1.6k
views
Mark Duplicates
picard
GATK
NGS
4.2 years ago by
priya.bmg
▴ 70
0
votes
0
replies
641
views
GenomicRatioSet object after minfi normalization does not show method used for preprocessing.
Illumina
minfi
EPIC
R
4.2 years ago by
samuel.carleial
• 0
0
votes
0
replies
1.2k
views
How to interpret scRNA-Seq cell dynamics from scVelo and CytoTrace results
velocyto
cell
cytotrace
rnaseq
dynamics
4.2 years ago by
gundalav
▴ 380
1
vote
2
replies
10k
views
TypeError: must be real number, not dict in python
string
python
dict
updated 4.2 years ago by
Joe
22k • written 4.2 years ago by
Georgia
• 0
3
votes
2
replies
1.7k
views
What cut-offs to use for Genomic Features Pie Chart for Methylation Array Data?
beadchip
array
methylation
4.2 years ago by
Pratik
★ 1.1k
3
votes
4
replies
1.6k
views
How many reads does Delly use for variant calling?
DNA-seq
bwa-mem
delly
bowtie2
updated 3.5 years ago by
archanaverma433
▴ 10 • written 4.2 years ago by
gt
▴ 30
2
votes
1
reply
2.3k
views
How to filter delly variants?
calling
DNA-seq
delly
variants
updated 4.2 years ago by
trausch
★ 2.0k • written 4.2 years ago by
gt
▴ 30
0
votes
1
reply
710
views
Finding Molecular function for more than 100 GO terms
Gene
Ontology
updated 4.2 years ago by
Pierre Lindenbaum
166k • written 4.2 years ago by
abhilashtripathi10
▴ 20
0
votes
0
replies
572
views
How to map the headers of a multiple sequence alignment of proteins file to their CDS counterparts from multiple files.
mutiple_alignment
peptide_files
cds_files
4.2 years ago by
Rijan
• 0
4
votes
2
replies
2.7k
views
Inserting Gaps into FASTA files for Alignment to Reference
mapping
Alignment
galaxy
FASTA
gap
updated 4.2 years ago by
Istvan Albert
103k • written 4.2 years ago by
lnrrnl
▴ 20
1
vote
2
replies
1.5k
views
Parsing issues with single cell file from GEO
cell
single
parsing
R
updated 4.2 years ago by
Kevin Blighe
89k • written 4.2 years ago by
iddryg
• 0
0
votes
0
replies
975
views
Clarifications about intercepts when fitting models with DESeq2
GLM
rnaseq
DESeq2
DEA
rna-seq
4.2 years ago by
Eisuan
▴ 20
0
votes
1
reply
1.1k
views
using a singualrity application ARGs-OAP
Data-Analysis
WholeShotgunMetagenome
AMR
Microbiome
Metagenomics
updated 4.2 years ago by
ATpoint
89k • written 4.2 years ago by
serene.s
• 0
4
votes
4
replies
3.0k
views
Single-stranded RNA-seq: strandedness of samples
rnaseq
4.2 years ago by
fr
▴ 220
3
votes
4
replies
3.3k
views
Choice of normalization method for spike-in data
spike-in
DiffBind
4.2 years ago by
eashby47
▴ 10
0
votes
1
reply
2.0k
views
Job:
Postdoctoral Position, Department of Biology , Colorado State University
postdoc
updated 2.6 years ago by
Ram
45k • written 4.2 years ago by
Anireddy
• 0
1
vote
6
replies
2.2k
views
How to group transcripts by "gene" from different transcript assemblies?
assembly
trinity
rnaspades
transcript
updated 4.2 years ago by
ponganta
▴ 590 • written 4.2 years ago by
O.rka
▴ 750
0
votes
7
replies
2.4k
views
How to get fold changes from MetaDE package in R?
R
MetaDE
updated 4.2 years ago by
ATpoint
89k • written 4.2 years ago by
humbertojirey
• 0
0
votes
1
reply
929
views
C. elegans WGS large portion of reads flagged as unmapped with Sam flag 133 and 165
sam
WGS
flag
133
165
unmapped
updated 4.2 years ago by
Tm
★ 1.1k • written 4.2 years ago by
tyler.j.kennedy
• 0
0
votes
0
replies
900
views
Help With Cbioportal expression data
rnaseq
TCGA
R
cbioportal
bioconductor
4.2 years ago by
daniela.paola.s.p
▴ 70
2
votes
2
replies
1.1k
views
Pathway Expression Analysis on Individual Cells?
seurat
sc-RNA-seq
4.2 years ago by
ospinae
• 0
0
votes
1
reply
1.0k
views
Protein homolog query issue
transcriptom
blast
species
sequence
Related
updated 4.2 years ago by
Jean-Karim Heriche
27k • written 4.2 years ago by
jaqx008
▴ 110
122,011 results • Page
606 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
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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…
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