Limit : all time
all time today this week this month this year
1,000 results • Page 4 of 20
Sort: Rank
Rank Views Votes Replies
0
votes
10
replies
530
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 6 days ago by 19k • written 14 days ago by • 0
0
votes
1
reply
145
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq nucleosome fragment
updated 14 days ago by 82k • written 14 days ago by • 0
0
votes
0
replies
99
views
Help with finding conferences in immuno-informatics/virology
virology conferences immunology
14 days ago by manaswwm ▴ 510
0
votes
0
replies
88
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
13 days ago by alifafiq1 • 0
0
votes
0
replies
94
views
How to get somatic variation based on RNA-seq data?
RNA-seq variation somatic
14 days ago by feather-W • 0
2
votes
4
replies
345
views
interpretartion of a vcf file
calling genotype ONT variant diploid
12 days ago by samuelkalandarov2002 ▴ 10
0
votes
0
replies
94
views
Annotating single cell data automatically
cell annotation single
14 days ago by Gerard • 0
0
votes
1
reply
180
views
RNA-seq bacteria contamination
RNA-seq
updated 14 days ago by 142k • written 14 days ago by • 0
0
votes
0
replies
85
views
Imputation advice
imputation
14 days ago by kl ▴ 10
0
votes
0
replies
107
views
Trimming best practices for SNP calling
trimming SNP trimmomatic
14 days ago by Enrique • 0
0
votes
0
replies
85
views
Correct way of reducing predictive model complexity
lasso glmnet predictvemodeling regression
14 days ago by sativus ▴ 20
0
votes
0
replies
93
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER MARINA ARACNe
14 days ago by Biostars2200 • 0
0
votes
0
replies
147
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 14 days ago by 8.7k • written 14 days ago by • 0
2
votes
5
replies
501
views
Marking duplicates using UMIs
Deduplication UMI
updated 14 days ago by 19k • written 15 days ago by • 0
0
votes
0
replies
149
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 15 days ago by 43k • written 15 days ago by • 0
0
votes
0
replies
156
views
Bacterial genome alignment with mauve
Bacteria mauve genome
15 days ago by rthapa ▴ 90
0
votes
0
replies
145
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation CGenFF Gromacs VMD
15 days ago by Mamatha Y S • 0
0
votes
2
replies
306
views
bam merging for archaic samples
samtools bam
updated 15 days ago by 43k • written 16 days ago by ▴ 100
1
vote
0
replies
553
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers TRINITY
16 days ago by mathavanbioinfo ▴ 90
0
votes
0
replies
233
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools gcs
16 days ago by abhishekghadge • 0
2
votes
5
replies
754
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 16 days ago by ▴ 760 • written 17 days ago by ★ 2.4k
0
votes
0
replies
201
views
agilent microarray gpl data does not have gene symbol column
microarray agilent gpl
updated 17 days ago by 43k • written 17 days ago by • 0
0
votes
0
replies
200
views
scRNA Cluster frequency
CV PCA scRNA Cluster-Frequency
17 days ago by Nitin • 0
0
votes
0
replies
195
views
Chemical structure validation
structure cap validation metabolite
17 days ago by Rodolfo Adrián • 0
0
votes
1
reply
290
views
Downloading the raw microarray data from GEO
.gpr microarray .CEL
updated 17 days ago by 142k • written 17 days ago by ▴ 10
0
votes
0
replies
220
views
Copy number variation plot
Copy-number-variation genomics
updated 17 days ago by 43k • written 17 days ago by • 0
0
votes
0
replies
196
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs ngsTools ANGSD genomics
17 days ago by DanielEB_fisk ▴ 20
0
votes
1
reply
306
views
Could you please assist in identifying this cluster?
single-cell
updated 17 days ago by 43k • written 17 days ago by ▴ 30
0
votes
0
replies
216
views
Conversion to tree format
PLINK bed Figtree SplitsTree
updated 17 days ago by 43k • written 17 days ago by • 0
0
votes
0
replies
211
views
miRDeep2: How to get the read counts
mirdeep2
17 days ago by Atul K. • 0
0
votes
0
replies
214
views
Lncipedia GTF file error
Proteomics
updated 17 days ago by 43k • written 17 days ago by ▴ 30
3
votes
3
replies
525
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 16 days ago by 14k • written 17 days ago by ▴ 580
0
votes
2
replies
575
views
How to get the reference panel for UKBB
UKBB GWAS clump
17 days ago by 航太郎 • 0
0
votes
0
replies
228
views
create genewise sync file in popoolation
popoolation
updated 18 days ago by 142k • written 18 days ago by • 0
0
votes
2
replies
406
views
error in coding potential calculator CPC2
cpc CPC2 coding-potential
17 days ago by Ashok • 0
0
votes
2
replies
451
views
miRNAs quantification using mirdeep2 tool
differential-expression mirdeep2 miRNA
17 days ago by Ashok • 0
0
votes
0
replies
227
views
Variant Generation Using Longshot
long-reads variant-calling ONT minion longshot
updated 18 days ago by 43k • written 18 days ago by ▴ 10
0
votes
2
replies
456
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control SNV QC SNP
17 days ago by _quantum_girl_ ▴ 10
0
votes
0
replies
220
views
traying to make a maf from an already annotated vcf
vcf vcf2maf maf maftools VEP
14 days ago by Javier • 0
0
votes
0
replies
197
views
Pruning with plink finds a majority of SNPs in very high LD
LD SNP plink pruning
18 days ago by enferdeflame • 0
1
vote
1
reply
442
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA Limma
updated 15 days ago by ★ 7.1k • written 18 days ago by ▴ 260
0
votes
1
reply
415
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree microbiome
updated 18 days ago by 43k • written 19 months ago by • 0
0
votes
0
replies
169
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score tspex
updated 18 days ago by 43k • written 18 days ago by ▴ 10
0
votes
0
replies
190
views
How to root an unrooted tree with a known root tree?
phylogenetics rooting R
18 days ago by P. • 0
0
votes
0
replies
182
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
18 days ago by ekirsch • 0
1
vote
1
reply
493
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow python-apollo Apollo
17 days ago by renan.igor • 0
0
votes
0
replies
202
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
18 days ago by synat.keam ▴ 100
0
votes
1
reply
293
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 19 days ago by 142k • written 19 days ago by • 0
0
votes
4
replies
628
views
Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
17 days ago by Kai Xin • 0
1
vote
1
reply
248
views
Retrieve a % coverage for each transcript
RNA-seq
updated 19 days ago by 43k • written 19 days ago by ▴ 40
1,000 results • Page 4 of 20
Recent Votes
How to save GRanges object to csv file
Answer: How to get proteins from GFF file resulted from MAKER annotation
Answer: Gene ontology and homologs
Comment: anRichment is missing
Comment: Gene Specific coverage from WGS data
Comment: Gene Specific coverage from WGS data
Comment: High Malat-1 expression in single cell data
Recent Locations • All
United States, just now
Spain, 1 minute ago
USA, 2 minutes ago
Uruguay, 3 minutes ago
United States, 4 minutes ago
United States, 5 minutes ago
United States, 5 minutes ago
Recent Awards • All
Popular Question to Scott McKay ▴ 30
Popular Question to A. Domingues ★ 2.7k
Scholar to LChart 3.9k
Popular Question to JACKY ▴ 140
Popular Question to bhumm ▴ 140
Teacher to Matthias Zepper 4.6k
Popular Question to sidrah.maryam ▴ 50
Recent Replies
Answer: Where to get the following bed file? by LChart 3.9k
UCSC maintains a list of exome probe sets and targets. You could check there: https://hgdownload.soe.ucsc.edu/gbdb/hg19/exomeProbesets/
Comment: How to compute TPM normalized values for TCGA miRNA data? by Ngrin • 0
Yes, I found some similar ideas on biostar repository. So you think the authors have done something wrong? And I should only consider CPM?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by Chris Dean ▴ 390
It is difficult to answer how they were able to identify *S. hominis* without seeing the code or paper. To address your second question, i…
Comment: Problem with Seurat package in PercentageFeatureSet function by bk11 ★ 2.4k
Did you check where the `features.tsv.gz` file had Gene IDs or Ensembl IDs?
Answer: How to compute TPM normalized values for TCGA miRNA data? by dsull ★ 6.0k
TPM is irrelevant for miRNA-seq; CPM works fine. TPM tries to adjust for length effects by dividing by gene length (e.g. reducing the im…
Comment: Applying the metacell2 algorithm using python by Wayne ★ 2.0k
"I'm also unsure what qualifies as a lateral gene." The [README where you reference](https://metacells.readthedocs.io/en/latest/readme.htm…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 90
Ah, yes this makes sense! I knew this was an issue with, say, using kraken2 on shotgun metagenomic reads, but I don't have a lot of experi…
Comment: How to access TCGA samples that were treated with a specific drug? by Qroid ▴ 40
Thank you. Maybe it's best to confirm with the authors about how they're getting responder/non-responder labels. I'll do that now.
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by Chris Dean ▴ 390
If you sequenced a short hypervariable region, most of your sequence reads will not be able to be assigned to the species level. One possi…
Comment: anRichment is missing by GenoMax 142k
Consider emailing Dr. Horvath about this. Until enough people make him aware of this issue WGCNA "problem" is unlikely to get fixed.
Comment: anRichment is missing by Tatyana • 0
Unfortunately, there are only tutorials and codes for tutorials for WGCNA, not installation files for any their packages... :(
Comment: anRichment is missing by GenoMax 142k
See this link for the WGCNA documentation and code from Peter Langfelder : https://bioinformatics.stackexchange.com/questions/21885/where-t…
Comment: anRichment is missing by Tatyana • 0
The problem is back, Horwath's lab web is down again. Is it possible to get anRichment istallation file somewhere? (The greater problem is …
Comment: 16S rRNA microbiome differential abundance analysis with DESeq2 finds same micro by andres.firrincieli 3.6k
1. Maribaculaceae is a family not a genus 2. Who said that ASV with the same taxonomic classification must have the same behaviour? 3. With…
Comment: Question regarding WGCNA by andres.firrincieli 3.6k
the within-group variability is so small that these look like technical replicates rather than independent biological replicates
Traffic: 2661 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