Limit : this week
all time today this week this month this year
287 results • Page 2 of 6
Sort: replies
Rank Views Votes Replies
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 3 days ago by • 0 • written 6.5 years ago by ▴ 30
1
vote
5
replies
683
views
RNA seq differential expression analysis
RNA-seq normalization
updated 4 days ago by ★ 1.7k • written 5 days ago by • 0
1
vote
5
replies
540
views
Duplicate marking, read names, and the SRA
SRA MarkDuplicates
updated 4 days ago by 141k • written 4 days ago by • 0
1
vote
5
replies
279
views
DYH17 Structure Prediction
BLAST Protein-Structure-Prediction
15 hours ago by anasjamshed ▴ 120
1
vote
5
replies
578
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode MGI DNBelab single-cell
updated 12 hours ago by • 0 • written 3 months ago by • 0
2
votes
5
replies
1.9k
views
Differential Expression Analysis with batches which have different biological groups
R RNA-Seq limma DE batch-effect
updated 6 days ago by 43k • written 4.8 years ago by ▴ 60
3
votes
5
replies
523
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
1 day ago by n_navy • 0
8
votes
5
replies
4.7k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by ▴ 60
2
votes
5
replies
422
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats hg002 bed homopolymer-regions
6 days ago by Bikram Kumar • 0
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 6 days ago by • 0 • written 4.6 years ago by ▴ 40
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq batch-effect Random-Forest
updated 6 days ago by 43k • written 4.7 years ago by ▴ 10
0
votes
4
replies
504
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq gene-expression
updated 3 days ago by 82k • written 4 days ago by ▴ 140
4
votes
4
replies
2.6k
views
Advice on Handling Batch Effect in ChIP-seq Experiment
ChIP-Seq batch-effect sequencing
updated 6 days ago by 43k • written 4.6 years ago by ▴ 20
5
votes
4
replies
612
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq EdgeR DEGs DESeq2
5 days ago by BioinfGuru ★ 1.7k
2
votes
4
replies
4.5k
views
Differential Expression Analysis with monocle and batch effect correction
single-cell RNA-Seq batch-effect
updated 6 days ago by 43k • written 5.9 years ago by ▴ 60
2
votes
4
replies
6.0k
views
Batch Effect Removal in RNA-Seq Data for DGE & WGCNA. Should I omit any samples according to PCA plots?
Batch-effect RNA-Seq R DESeq2
updated 5 days ago by 43k • written 7.6 years ago by ▴ 70
3
votes
4
replies
630
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
1 day ago by rahu • 0
1
vote
4
replies
368
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus GTF
updated 2 hours ago by • 0 • written 5 months ago by • 0
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq RNA-Seq batch-effect DESeq2
updated 6 days ago by 43k • written 5.1 years ago by ★ 2.6k
2
votes
4
replies
240
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
3 hours ago by HyperEvo • 0
1
vote
4
replies
13k
views
RNA sequencing data batch effect removal
RNA-Seq batch-effect
updated 5 days ago by 43k • written 7.4 years ago by • 0
5
votes
4
replies
551
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
54 minutes ago by kirillkirilenko ▴ 40
1
vote
4
replies
674
views
What happened to Tombo Re-squiggle
Tombo resquiggle ONT
updated 5 days ago by 43k • written 3 months ago by • 0
0
votes
4
replies
1.2k
views
Batch effects
Batch-effect transcriptomics
updated 5 days ago by 43k • written 2.6 years ago by ▴ 30
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 5 days ago by 43k • written 18 months ago by • 0
1
vote
4
replies
1.4k
views
Removing/Accounting for batch effects in unbalanced group RNAseq data
rna-seq batch-effect deseq
updated 5 days ago by 43k • written 2.2 years ago by • 0
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect omniexpress GWAS GSA
updated 6 days ago by 43k • written 4.8 years ago by ▴ 10
0
votes
4
replies
205
views
Should I use unpaired reads from trimmomatic
RNA-seq QC Trimmomatic
updated 7 hours ago by 14k • written 1 day ago by • 0
3
votes
4
replies
416
views
biomaRt error for different R version
biomaRt R
updated 5 days ago by 141k • written 6 days ago by ▴ 490
1
vote
4
replies
3.1k
views
remove batch effect for multiple tumor data
RNA-Seq batch-effect
updated 5 days ago by 43k • written 7.1 years ago by ▴ 40
0
votes
4
replies
1.8k
views
Correcting batch effect in unevenly distributed groups
RNA-Seq batch-effect R
updated 6 days ago by 43k • written 4.8 years ago by ▴ 20
0
votes
4
replies
569
views
Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
5 days ago by Kai Xin • 0
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R RNA-Seq combat python batch-effect
updated 5 days ago by 43k • written 7.1 years ago by ▴ 310
0
votes
4
replies
487
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx deconcolution
5 days ago by feather-W • 0
1
vote
4
replies
1.7k
views
Batch correction and DE analysis of miRNA Seq data
miRNAseq Differential-Expression batch-effect
updated 5 days ago by 43k • written 5.1 years ago by ▴ 50
0
votes
4
replies
188
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
updated 15 hours ago by 141k • written 17 hours ago by ▴ 20
2
votes
3
replies
302
views
How to establish haplotype-specific gene expression levels
RNA-seq Haplotype
updated 1 day ago by ★ 5.8k • written 14 days ago by ▴ 60
3
votes
3
replies
162
views
Genbank vs SRA
ncbi genbank genomics sra
updated 1 day ago by ★ 27k • written 1 day ago by ▴ 520
3
votes
3
replies
493
views
Korean human genome reference file
GWAS reference imputation
5 days ago by SeoGyun • 0
2
votes
3
replies
936
views
Method to detect genome doubling
CNV genome doubling
updated 1 day ago by 4.2k • written 4.5 years ago by ▴ 750
3
votes
3
replies
706
views
KissDE and batch effect
kissDE kissplice
1 day ago by david.b.rombaut ▴ 10
3
votes
3
replies
190
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide Genomic Sequence Uniprot Proteins
updated 1 day ago by 141k • written 1 day ago by ▴ 10
1
vote
3
replies
2.0k
views
gene expression data analysis and batch effect methods
microarray Gene-expression batch-effect
updated 5 days ago by 43k • written 6.9 years ago by ▴ 220
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat CNA Batch-Effect
updated 6 days ago by 43k • written 5.5 years ago by ▴ 150
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq batch-effect sequencing
updated 5 days ago by 43k • written 6.9 years ago by • 0
1
vote
3
replies
288
views
Merging vcf files with bcftools ([E::get_intv] Failed to parse TBX_VCF, was wrong -p [type] used?)
vcf tabix bcftools
updated 6 days ago by 161k • written 12 days ago by • 0
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink PED
updated 1 day ago by 10k • written 6.1 years ago by ▴ 10
7
votes
3
replies
4.5k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA RNA-Seq batch-effect
updated 6 days ago by 43k • written 5.1 years ago by ▴ 100
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor limma sva r batch-effect
updated 5 days ago by 43k • written 7.6 years ago by ★ 1.2k
1
vote
3
replies
3.3k
views
How to correct for batch effect in microarray meta-analysis
ComBat microarray meta-analysis batch-effect
updated 5 days ago by 43k • written 9.9 years ago by ▴ 120
287 results • Page 2 of 6
Recent Votes
Comment: Per base sequence content error in RNAseq analysis
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
Comment: TCGA2STAT Error: Firehose connection
Answer: HaplotypeCaller - only SNPs
Recent Locations • All
Russia, 2 minutes ago
South Korea, 3 minutes ago
India, 8 minutes ago
Canada, 9 minutes ago
Russia, 13 minutes ago
India, 13 minutes ago
United States, 15 minutes ago
Recent Awards • All
Popular Question to subhiksha ▴ 30
Popular Question to v.berriosfarias ▴ 140
Popular Question to AdviceSeeker • 0
Great Question to Ann ★ 2.4k
Scholar to marco.barr ▴ 80
Popular Question to Kash ▴ 110
Scholar to GenoMax 141k
Recent Replies
Comment: How to compare the quality of assemblies by kirillkirilenko ▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by Istvan Albert 100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs by analyst ▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus by atowns21 • 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t by yxwucq • 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error? by Mensur Dlakic ★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks? by HyperEvo • 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus by GenoMax 141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database by Art1ess • 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection by LauferVA 4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
Comment: Redirection of Duplicate PMIDs by LauferVA 4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus by atowns21 • 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs by Pierre Lindenbaum 161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
Answer: Gene set enrichment analysis differences between 2020 and 2024 by geneontologyhelp ▴ 380
We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
Traffic: 1840 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