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1,082 results • Page
1 of 22
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How to assign cell types after integration in scRNA
integration
conditions
ScRNA
seq
just now by
Francesco
▴ 10
0
votes
0
replies
8
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
just now by
tnminh89
▴ 10
1
vote
2
replies
39
views
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 1 minute ago by
ATpoint
82k • written 2 hours ago by
noodle
▴ 520
0
votes
0
replies
12
views
Extract protein sequence
fasta
alighment
blast
1 hour ago by
anna
▴ 20
0
votes
0
replies
14
views
Filter low express genes in microarray data
microarray
1 hour ago by
Chris
▴ 260
0
votes
1
reply
214
views
absolute path for symbolic links in Snakefile
Snakemake
updated 2 hours ago by
Jesse
▴ 740 • written 8 days ago by
yifangt86
▴ 60
0
votes
2
replies
207
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 2 hours ago by
Jesse
▴ 740 • written 2 days ago by
Broccoli
• 0
2
votes
3
replies
193
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 3 hours ago by
Arup Ghosh
3.2k • written 1 day ago by
chaco001
▴ 40
0
votes
2
replies
157
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
4 hours ago by
O.rka
▴ 710
0
votes
1
reply
125
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 17 hours ago by
Gordon Smyth
★ 7.0k • written 1 day ago by
hagl
▴ 10
0
votes
2
replies
160
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
11 hours ago by
Guille
• 0
1
vote
1
reply
120
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
updated 22 hours ago by
Gordon Smyth
★ 7.0k • written 1 day ago by
pairedttest
▴ 10
2
votes
6
replies
1.9k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 21 hours ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
0
votes
0
replies
234
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
23 hours ago by
biocellbio
• 0
4
votes
8
replies
488
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 17 hours ago by
Alex Reynolds
35k • written 1 day ago by
J
▴ 10
4
votes
7
replies
549
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 15 hours ago by
dsull
★ 5.8k • written 4 days ago by
qudrat.nii
▴ 10
0
votes
0
replies
86
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 1 day ago by
Ram
43k • written 1 day ago by
vanbelj
▴ 40
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
226
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 1 day ago by
dsull
★ 5.8k • written 1 day ago by
Aaliya
▴ 10
3
votes
0
replies
125
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 1 day ago by
Claire Watson
▴ 60
0
votes
2
replies
194
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 1 day ago by
Ram
43k • written 1 day ago by
The_PyPanda
▴ 10
0
votes
0
replies
128
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
1 day ago by
HarperReed
• 0
3
votes
3
replies
197
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 1 day ago by
GenoMax
141k • written 1 day ago by
sapuizait
▴ 10
1
vote
0
replies
93
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
1 day ago by
KABILAN
▴ 50
0
votes
0
replies
100
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 1 day ago by
Ram
43k • written 1 day ago by
SineWave
• 0
0
votes
0
replies
99
views
RNA-seq: full length gene
RNA-seq
updated 1 day ago by
Ram
43k • written 1 day ago by
Nargis
• 0
1
vote
3
replies
188
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 4 hours ago by
Jeremy Leipzig
22k • written 1 day ago by
zihanss
• 0
0
votes
0
replies
88
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
1 day ago by
turcoa1
• 0
3
votes
3
replies
219
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 1 day ago by
swbarnes2
14k • written 2 days ago by
M
• 0
0
votes
0
replies
103
views
Designing single-stable RNA molecules
structure
RNA
2 days ago by
Edna
• 0
0
votes
0
replies
117
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
2 days ago by
simplitia
▴ 130
0
votes
1
reply
153
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
212
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Begonia_pavonina
▴ 150
0
votes
2
replies
242
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 1 day ago by
Ram
43k • written 2 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
182
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
updated 2 days ago by
Ram
43k • written 2 days ago by
Francesco
▴ 10
1
vote
6
replies
337
views
ScRNA data question
scRNA
Vlnplot
Samples
10 hours ago by
starswillfade
▴ 10
0
votes
0
replies
117
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
110
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
106
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
2 days ago by
Emily
▴ 10
1
vote
0
replies
127
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
111
views
how to read graph_test output of monocle 3
monocle3
2 days ago by
synat.keam
▴ 100
0
votes
0
replies
140
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
2 days ago by
Assaf
• 0
0
votes
1
reply
439
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
277
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
2 days ago by
QX
• 0
2
votes
1
reply
197
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 2 days ago by
Adrian Altenhoff
★ 1.1k • written 3 days ago by
hemantcnaik
• 0
0
votes
0
replies
121
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
2 days ago by
Aspire
▴ 300
2
votes
4
replies
290
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
updated 2 days ago by
Ram
43k • written 2 days ago by
ashaneev07
▴ 20
2
votes
3
replies
237
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
analyst
▴ 30
0
votes
3
replies
258
views
Highest variable features in single cell data
single-cell
updated 1 day ago by
bk11
★ 2.4k • written 2 days ago by
Kazo
• 0
0
votes
1
reply
208
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 2 days ago by
Scooter
▴ 280 • written 3 days ago by
Akash D
▴ 40
1,082 results • Page
1 of 22
Recent Votes
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
NGS forensics: how to know if data is fabricated
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
How do I find out the read lenght of a fastq file?
Calculate Allele balance by sample
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
Answer: Is there a tool that sorts gtf files?
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Recent Replies
Comment: NGS forensics: how to know if data is fabricated
by
ATpoint
82k
My first question would be how strong your background in such analysis is. Claim of fabrication is very serious, so be 100% sure to back it…
Answer: NGS forensics: how to know if data is fabricated
by
Jeremy Leipzig
22k
This is a super-interesting question from an algorithmic standpoint (devising a model that can distinguish real from synthetic reads) but I…
Answer: absolute path for symbolic links in Snakefile
by
Jesse
▴ 740
It's nothing to do with Snakemake, just the ordinary confusion of making relative symlinks when your working directory is somewhere else. …
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
by
Jesse
▴ 740
[seqmagick](https://github.com/fhcrc/seqmagick/) has a `--squeeze-threshold` option that does just this. For example with an MSA of five s…
Comment: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
Arup Ghosh
3.2k
Use the standalone version of Nextflow and specify the process-specific conda environments paths.
Comment: gvcf joint calling
by
Jeremy Leipzig
22k
can you show us an exonic position in your VCF file that is all `./.`?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
O.rka
▴ 710
Thank you. This answers my question. The reason I am asking is because I’m trying to do set enrichment analysis with BRENDA pathways using…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
colindaven
6.4k
I used to use nextflow in a conda env. That requires the env to be active when a pipeline is started. Also I have productive pipelines whic…
Comment: different FeatureCounts output for the same data
by
Istvan Albert
100k
just to clarify, it is not that the program algorithm works differently but the meaning of the flags changed; before -p was sufficient to…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
Comment: ScRNA data question
by
starswillfade
▴ 10
features <- SelectIntegrationFeatures(object.list = merged_dat) data.anchors <- FindIntegrationAnchors(object.list = merged_dat, …
Comment: gvcf joint calling
by
zihanss
• 0
Thank you for your help! I really appreciate it! And you know, the merged WES gVCF files still have "NA" loci. For such cases, I am quite …
Comment: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Guille
• 0
Thank you for your answer! The MDS plot seems to group most treatment groups close-by, so I'm starting to suspect the effect of treatment …
Answer: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
Mensur Dlakic
★ 27k
They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
Comment: Heatmap and rna-seq
by
dsull
★ 5.8k
https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
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