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442 results • Page
4 of 9
Sort: replies
Rank
Views
Votes
Replies
0
votes
2
replies
219
views
Can't figure out plink --sample-diff
plink
26 days ago by
curious
▴ 750
0
votes
2
replies
282
views
Regions not clear in VCF
whole-exome
variant-calling
updated 28 days ago by
Ram
43k • written 29 days ago by
priya.bmg
▴ 60
1
vote
2
replies
308
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 19 days ago by
Ram
43k • written 19 days ago by
aniigodwinn
• 0
0
votes
2
replies
276
views
Bedmethyl file format
bedmethyl
methylation
updated 19 days ago by
GenoMax
142k • written 19 days ago by
njornet
▴ 20
1
vote
2
replies
341
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 21 days ago by
Istvan Albert
100k • written 22 days ago by
Jiang
• 0
5
votes
2
replies
1.8k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 20 days ago by
Ram
43k • written 3.0 years ago by
Mat
▴ 60
0
votes
2
replies
406
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
17 days ago by
Ashok
• 0
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 18 days ago by
Ram
43k • written 6.6 years ago by
Alternative
▴ 270
1
vote
2
replies
266
views
alignment result
RNA-seq
samtools
hisat2
11 days ago by
ahmad.sajad4541
• 0
0
votes
2
replies
240
views
Downloading older version of a tool
Alignment
tools
2 days ago by
Ruqaiya
• 0
1
vote
2
replies
818
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 20 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
0
votes
2
replies
566
views
autodockvina
python
python3
autodock
updated 18 days ago by
Ram
43k • written 4 months ago by
iamsmor
• 0
1
vote
2
replies
228
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 6 days ago by
Ram
43k • written 6 days ago by
Ravita
• 0
2
votes
2
replies
207
views
PDB related issue
rcsb
pdb
updated 7 days ago by
noodle
▴ 580 • written 8 days ago by
Nafi
• 0
2
votes
2
replies
183
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
updated 10 hours ago by
GenoMax
142k • written 6 days ago by
Adyasha
• 0
1
vote
2
replies
262
views
permutation test in edgeR
rna-seq
edgeR
updated 14 days ago by
Gordon Smyth
★ 7.1k • written 28 days ago by
Netanel
• 0
0
votes
2
replies
407
views
How can I solve this error?
metal
18 days ago by
22211020193
• 0
0
votes
1
reply
188
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 12 days ago by
Sofia
• 0 • written 12 days ago by
mawigoj318
• 0
0
votes
1
reply
290
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 17 days ago by
GenoMax
142k • written 17 days ago by
bioyas
▴ 10
0
votes
1
reply
228
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 2 days ago by
Thanujay S
• 0 • written 3 days ago by
yahn
• 0
1
vote
1
reply
245
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 11 days ago by
ATpoint
82k • written 11 days ago by
AaronJaime
• 0
0
votes
1
reply
180
views
RNA-seq bacteria contamination
RNA-seq
updated 14 days ago by
GenoMax
142k • written 14 days ago by
sh
• 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
Gordon Smyth
★ 7.1k • written 18 days ago by
Chris
▴ 260
0
votes
1
reply
415
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 18 days ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
1
vote
1
reply
199
views
Failed kmer content
kmer
illumina
ngs
updated 13 days ago by
Ram
43k • written 13 days ago by
Kasturi
• 0
3
votes
1
reply
279
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 24 days ago by
Ram
43k • written 25 days ago by
rj.rezwan
• 0
0
votes
1
reply
306
views
Could you please assist in identifying this cluster?
single-cell
updated 17 days ago by
Ram
43k • written 17 days ago by
carolofharvest
▴ 30
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 19 days ago by
Ram
43k • written 6.3 years ago by
jjrin
▴ 40
0
votes
1
reply
544
views
HOMER on AWS
HOMER
updated 3 days ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
1
vote
1
reply
664
views
Save experiment with batch effects - Protein microarray
statistics
protein-array
batch-effect
updated 19 days ago by
Ram
43k • written 4.4 years ago by
s.lima.diogenes
▴ 10
1
vote
1
reply
199
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 20 days ago by
dsull
★ 6.0k • written 20 days ago by
niruf
• 0
0
votes
1
reply
240
views
How do I know whether it is not a failure of ChIPseq data
ChIPseq
updated 29 days ago by
dthorbur
★ 1.9k • written 4 weeks ago by
Herman Einstein
• 0
0
votes
1
reply
1.2k
views
Controlling for batch effect in SNP-based PCA
whole-genome
PCA
batch-effect
SNP
updated 19 days ago by
Ram
43k • written 4.7 years ago by
Ace
▴ 90
0
votes
1
reply
187
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 2 days ago by
Ram
43k • written 3 days ago by
Valentina
• 0
0
votes
1
reply
148
views
Provean help
variant
Provean
updated 4 days ago by
Mensur Dlakic
★ 27k • written 4 days ago by
Arun Sai Kumar
• 0
0
votes
1
reply
273
views
How to do further funtional analysis of DEG KeggGet output list?
KEGGREST
DESEQ2
RNA-Seq
DEG
28 days ago by
joana.maclean
• 0
0
votes
1
reply
555
views
Differential Expression Analysis for miRNA
limma
Differential-gene-Expression
miRNA
updated 27 days ago by
Ram
43k • written 3.0 years ago by
Al
• 0
0
votes
1
reply
152
views
tbtool
tbtool
updated 14 days ago by
Ram
43k • written 14 days ago by
Raman
• 0
0
votes
1
reply
183
views
Help with DGEList function
DGEList
R
updated 1 day ago by
marco.barr
▴ 90 • written 2 days ago by
Natali
• 0
1
vote
1
reply
184
views
Failed to download data from EBI with ascp
EBI
aspera
updated 25 days ago by
GenoMax
142k • written 25 days ago by
biock
▴ 60
0
votes
1
reply
227
views
Subsetting and merging back Seurat Object brings different results
Seurat
4 days ago by
Bine
▴ 60
0
votes
1
reply
829
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 18 days ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
0
votes
1
reply
145
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 14 days ago by
ATpoint
82k • written 14 days ago by
enanoide
• 0
0
votes
1
reply
183
views
Differential Accessibility
DiffBind
updated 7 days ago by
Ram
43k • written 7 days ago by
Shloka
• 0
0
votes
1
reply
310
views
Monotonic genes in results of differential gene expression analysis
differential-expression
RNA-seq
monotonic-genes
updated 27 days ago by
Ram
43k • written 3 months ago by
Shaimaa Gamal
▴ 10
2
votes
1
reply
264
views
VEP annotation --per_gene allele choice
VEP
updated 24 days ago by
Ram
43k • written 24 days ago by
atariw
▴ 10
0
votes
1
reply
234
views
creating batch colum for batch correction
batch-correction
combat
12 hours ago by
Expert
▴ 10
0
votes
1
reply
285
views
cibersort. problem
cibersort
gema122
updated 28 days ago by
Ram
43k • written 4 weeks ago by
gem1
• 0
0
votes
1
reply
586
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 4 days ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
0
votes
1
reply
219
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 19 days ago by
DKA
▴ 40 • written 19 days ago by
james.melhorn
• 0
442 results • Page
4 of 9
Recent Votes
Comment: Which hg38 file?
Answer: Which hg38 file?
Answer: Where to get the following bed file?
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
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Recent Replies
Comment: Where to get the following bed file?
by
GenoMax
142k
SeqCap kits are discontinued. If you don't find the said file your will need to email Roche Support per this page: https://sequencing.roche…
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…
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