Limit : this month
all time today this week this month this year
975 results • Page 6 of 20
Sort: Votes
Rank Views Votes Replies
2
votes
4
replies
319
views
Addmetadata to seurat obj
seurat
26 days ago by synat.keam ▴ 100
2
votes
3
replies
365
views
How to establish haplotype-specific gene expression levels
RNA-seq Haplotype
updated 10 days ago by ★ 6.0k • written 27 days ago by ▴ 60
2
votes
1
reply
290
views
Pediococcus acidilactici sequence analysis
BLAST Gene-Ontology
updated 18 days ago by 43k • written 19 days ago by ▴ 120
2
votes
4
replies
365
views
Should I use unpaired reads from trimmomatic
RNA-seq QC Trimmomatic
updated 13 days ago by 14k • written 14 days ago by • 0
2
votes
4
replies
424
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 26 days ago by 142k • written 27 days ago by • 0
2
votes
2
replies
275
views
p-value in CIBERSORT
CIBERSORT p-value
5 days ago by michelafrancesconi9 ▴ 20
2
votes
1
reply
967
views
How to evaluate the performance of an RNA-seq pipeline
Differential-gene-expression RNA-Seq R DESeq2
updated 27 days ago by 43k • written 4.0 years ago by ▴ 310
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 19 days ago by 43k • written 7.4 years ago by • 0
2
votes
2
replies
955
views
Is there a file information dictionary for files downloaded from ENCODE through batch download?
ENCODE
updated 20 days ago by 43k • written 4.6 years ago by ▴ 40
2
votes
2
replies
314
views
Creating a cytoscape bubble figure
cytoscape network GO
25 days ago by Dave Carlson ★ 1.7k
2
votes
2
replies
405
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression edgeR
18 days ago by nhaus ▴ 310
2
votes
1
reply
1.2k
views
recommendation needed: scRNA-seq batch effect correction methods that can be used for differential expression
single-cell RNA-Seq batch-effect
updated 28 days ago by 43k • written 3.7 years ago by ▴ 70
2
votes
0
replies
221
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
21 days ago by Alexander ▴ 220
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
2
votes
5
replies
399
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
7 days ago by analyst ▴ 30
2
votes
2
replies
284
views
Association study using SNP data
Association Allele Parentage SNP
1 day ago by drajangirija • 0
2
votes
7
replies
5.3k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated 17 days ago by 82k • written 7.2 years ago by ▴ 80
2
votes
3
replies
940
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R RNA-Seq DE batch-effect GTEx
updated 21 days ago by 43k • written 4.1 years ago by ▴ 790
2
votes
6
replies
5.2k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq R seurat harmony batch-effect
updated 18 days ago by 43k • written 3.7 years ago by • 0
2
votes
2
replies
318
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 12 days ago by 43k • written 13 days ago by ▴ 140
2
votes
2
replies
201
views
MA plot of shrunken fold change
MA-plot Deseq2
updated 6 days ago by 82k • written 6 days ago by • 0
2
votes
4
replies
411
views
Which command ro run MAKER pipeline for gene annotation ?
run. command to MAKERpipeline.
updated 21 days ago by 142k • written 22 days ago by ▴ 10
2
votes
4
replies
355
views
SnpEff annotates coding duplication as intronic?
snpeff
19 days ago by kirill.zaslavsky • 0
2
votes
4
replies
376
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
12 days ago by HyperEvo • 0
2
votes
2
replies
367
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment gaps
updated 9 days ago by ▴ 760 • written 11 days ago by • 0
2
votes
5
replies
503
views
Creating an index from multiple .fsa files
HISAT2 BWA Alignment
27 days ago by theworldsagainstme • 0
2
votes
2
replies
292
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 25 days ago by 82k • written 25 days ago by ★ 9.4k
2
votes
6
replies
549
views
Correcting coordinates in gff3 file
awk unix gff3 python
updated 24 days ago by 4.6k • written 26 days ago by • 0
2
votes
9
replies
914
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 13 days ago by 4.2k • written 6 months ago by • 0
2
votes
3
replies
1.5k
views
Duplicate row name not allowed while reading the file in R
RNA-Seq deseq2 Differential-Gene-expression R
updated 27 days ago by 43k • written 4.9 years ago by • 0
2
votes
3
replies
274
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus annotation assembly genome
updated 3 days ago by ★ 1.9k • written 3 days ago by ▴ 30
2
votes
3
replies
795
views
Issues with Mixture file when using CIBERSORTx
Deconvolution CIBERSORTx
updated 2 days ago by • 0 • written 7 months ago by • 0
2
votes
0
replies
204
views
Tool: pySEACR
Peak-Calling CUT-and-RUN
25 days ago by Adam ▴ 30
2
votes
1
reply
264
views
VEP annotation --per_gene allele choice
VEP
updated 24 days ago by 43k • written 24 days ago by ▴ 10
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 15 days ago by 43k • written 10.6 years ago by ▴ 150
2
votes
2
replies
410
views
I am new to single cell analysis. Can RNA velocity (spliced/unspliced) be calculated solely from the raw file (count matrix) provided in the Suppleme…
GEO velocity count-matrix
updated 20 days ago by 43k • written 20 days ago by • 0
2
votes
1
reply
258
views
Trouble understanding seemingly contradicting results of GSE analysis (contradicting enriched GO terms with similar negative NES scores)
GSEA pathways GO-terms
updated 21 days ago by 19k • written 21 days ago by • 0
2
votes
6
replies
500
views
KEGG analysis in R
KEGG clusterProfiler Zea-mays
25 days ago by sansan_96 ▴ 80
2
votes
2
replies
1.1k
views
Can we directly use batch corrected gene expression (Bulk RNA-seq) for further downstream analyses?
RNA-Seq batch-effect
updated 18 days ago by 43k • written 5.0 years ago by ▴ 60
2
votes
4
replies
1.2k
views
PLINK p value returning NA
GWAS PLINK
updated 28 days ago by 10k • written 19 months ago by • 0
2
votes
0
replies
123
views
News: Course Functional Programming with R
Rstats TScourses Rproject KeepLearning Rlang
26 days ago by Transmitting Science communication ▴ 70
2
votes
3
replies
979
views
Method to detect genome doubling
CNV genome doubling
updated 14 days ago by 4.2k • written 4.5 years ago by ▴ 750
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression RNA-Seq DESeq2
updated 27 days ago by 43k • written 8.1 years ago by ▴ 80
2
votes
2
replies
267
views
latest dbSNP (ncbi) which genome assembly
ncbi dbSNP assembly genome
28 days ago by jaime alvarez ▴ 30
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi metagenomics centrifuge gi_taxid_nucl.dmp taxonomy
updated 11 days ago by • 0 • written 2.5 years ago by • 0
2
votes
3
replies
493
views
Tool: DEGap - an online tool for Differential Gene Expression analysis
degap
27 days ago by Anastasia ▴ 10
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray combat batch-effect median-normalization
updated 18 days ago by 43k • written 18 months ago by • 0
2
votes
2
replies
638
views
Batch correction for DE analysis
batch-correction mRNA RNA-seq DEGs MDSplot
updated 20 days ago by 43k • written 2.6 years ago by ▴ 10
2
votes
1
reply
255
views
Finding orthologs between genome error
OMA OMAbrowser
updated 11 days ago by ★ 1.1k • written 12 days ago by • 0
2
votes
0
replies
1.8k
views
ComBat-seq adjustment of batch effects
RNA-Seq ComBat-seq SVA edgeR batch-effect
updated 19 days ago by 43k • written 3.5 years ago by ▴ 50
975 results • Page 6 of 20
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
Recent Locations • All
Portugal, just now
Palau, 1 minute ago
United States, 3 minutes ago
United States, 7 minutes ago
Moscow, 9 minutes ago
United States, 11 minutes ago
United States, 14 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: Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genom by LChart 3.9k
Step 1: Go to TCGA in the GDC and open the Cohort Builder https://portal.gdc.cancer.gov/analysis_page?app=CohortBuilder&tab=general Step …
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 …
Traffic: 1527 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