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286 results • Page 4 of 6
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350
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer ATAC-seq
6 days ago by Ronin • 0
0
votes
1
reply
180
views
Freyja plot error
Freyja
updated 6 days ago by 43k • written 6 days ago by • 0
0
votes
3
replies
1.1k
views
Discrepancy between E() Values in Blastp Search - HELP
BLAST E-value Blastp Protein
updated 6 days ago by 43k • written 5.3 years ago by • 0
0
votes
2
replies
364
views
Which experiments generate Position Frequency Matrix?
Position-Frequency-Matrix
6 days ago by arriyaz.nstu ▴ 30
0
votes
1
reply
338
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics bootstrap
updated 6 days ago by ▴ 150 • written 12 days ago by ▴ 40
0
votes
0
replies
161
views
Struggling to lift genome builds
PLINK liftover GWAS
updated 6 days ago by 141k • written 6 days ago by • 0
0
votes
2
replies
1.4k
views
Interpretation problem at PCA plot for detecting batch effect
PCA RNA-Seq batch-effect
updated 6 days ago by 43k • written 4.4 years ago by ▴ 170
0
votes
1
reply
1.2k
views
Controlling for batch effect in SNP-based PCA
whole-genome PCA batch-effect SNP
updated 6 days ago by 43k • written 4.7 years ago by ▴ 90
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
1
reply
829
views
How to compare differentially expressed genes among different affymatrix dataset
microarray batch-effect R
updated 6 days ago by 43k • written 4.8 years ago by ▴ 30
0
votes
2
replies
2.9k
views
Should I pre-normalize RNAseq data before combat?
RNA-Seq combat batch-effect R
updated 6 days ago by 43k • written 4.8 years ago by ▴ 50
0
votes
0
replies
1.1k
views
Should batch correction be performed before or after feature selection in scRNA-seq
batch-effect scRNA-seq feature-selection
updated 6 days ago by 43k • written 4.9 years ago by ▴ 140
0
votes
0
replies
1.7k
views
Batch effect and CCA
CCA RNA-Seq seurat batch-effect
updated 6 days ago by 43k • written 5.1 years ago by ▴ 110
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
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect R
updated 6 days ago by 43k • written 6.1 years ago by • 0
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva batch-effect
updated 6 days ago by 43k • written 6.2 years ago by ▴ 40
0
votes
1
reply
261
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 6 days ago by 141k • written 6 days ago by • 0
0
votes
0
replies
169
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
6 days ago by synat.keam ▴ 100
0
votes
2
replies
361
views
How can I solve this error?
metal
6 days ago by 22211020193 • 0
0
votes
0
replies
163
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
6 days ago by ekirsch • 0
0
votes
4
replies
489
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx deconcolution
6 days ago by feather-W • 0
0
votes
0
replies
171
views
How to root an unrooted tree with a known root tree?
phylogenetics rooting R
6 days ago by P. • 0
0
votes
2
replies
305
views
GSEA analysis in R
GSEA R Arabidopsis
6 days ago by Sudip • 0
0
votes
2
replies
337
views
How to add motifs in cellranger-arc reference?
gtf scRNAseq fasta cellranger
updated 5 days ago by • 0 • written 9 weeks ago by ▴ 150
0
votes
1
reply
262
views
10x VDJ (TCR/BCR) BAM to fastq
TCR VDJ BCR 10x
updated 5 days ago by 141k • written 5 days ago by ★ 1.9k
0
votes
1
reply
397
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree microbiome
updated 5 days ago by 43k • written 19 months ago by • 0
0
votes
1
reply
260
views
DEseq2
RNA-seq DESeq2
updated 5 days ago by 43k • written 6 days ago by • 0
0
votes
0
replies
183
views
News: Online course: Meta-analysis in R
Meta-Analysis Statistics R
updated 5 days ago by 43k • written 5 days ago by ★ 2.5k
0
votes
0
replies
169
views
News: Course - Agent-Based Modelling Using NetLogo - University of Lodz, Poland
Netlogo Individual-Based-Models Agent-Based-Models
updated 5 days ago by 43k • written 5 days ago by ★ 2.5k
0
votes
0
replies
155
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score tspex
updated 5 days ago by 43k • written 6 days ago by ▴ 10
0
votes
0
replies
172
views
Pruning with plink finds a majority of SNPs in very high LD
LD SNP plink pruning
5 days ago by enferdeflame • 0
0
votes
0
replies
207
views
Variant Generation Using Longshot
long-reads variant-calling ONT minion longshot
updated 5 days ago by 43k • written 5 days ago by ▴ 10
0
votes
2
replies
1.2k
views
Normalization (microarray data)
microarray Normalization Batch-effect
updated 5 days ago by 43k • written 6.3 years ago by ▴ 20
0
votes
1
reply
2.9k
views
Microarray batch effect correction
Microarray Batch-effect
updated 5 days ago by 43k • written 6.6 years ago by ▴ 100
0
votes
1
reply
1.8k
views
Advice required for remove batch effect which perfectly collinear with contrast of interest
RNA-seq batch-effect
updated 5 days ago by 43k • written 6.6 years ago by ▴ 80
0
votes
0
replies
2.0k
views
NOISeq Batch Correction to RNA-seq data
Batch-effect RNA-Seq ARSyNseq limma NOISeq
updated 5 days ago by 43k • written 6.9 years ago by • 0
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma RNA-Seq edgeR batch-effect
updated 5 days ago by 43k • written 7.0 years ago by • 0
0
votes
0
replies
1.9k
views
Correcting batch effect from known variables in RnBeads using Combat
Combat 450k methylation RnBeads batch-effect
updated 5 days ago by 43k • written 7.1 years ago by ▴ 40
0
votes
0
replies
1.9k
views
batch effect in radseq
radseq batch-effect SNP
updated 5 days ago by 43k • written 7.5 years ago by ▴ 50
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
0
votes
0
replies
729
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq scRNA-Seq batch-effect
updated 5 days ago by 43k • written 3.4 years ago by ▴ 180
0
votes
1
reply
815
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR Batch-effect RNA-Seq
updated 5 days ago by 43k • written 3.7 years ago by • 0
0
votes
7
replies
1.9k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering dendrogram RNA-Seq batch-effect
updated 5 days ago by 43k • written 4.0 years ago by ▴ 500
0
votes
0
replies
1.2k
views
Batch estimate using kBET
batch-effect kbet
updated 5 days ago by 43k • written 4.0 years ago by • 0
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression transcriptome
updated 5 days ago by 43k • written 9.0 years ago by • 0
0
votes
0
replies
1.8k
views
Differential expression using Scran batch corrected data
single-cell Batch-effect RNA-Seq Scran
updated 5 days ago by 43k • written 5.4 years ago by ▴ 10
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat R SVA Biostatistics batch-effect
updated 5 days ago by 43k • written 7.4 years ago by • 0
0
votes
2
replies
534
views
autodockvina
python python3 autodock
updated 5 days ago by 43k • written 3 months ago by • 0
0
votes
0
replies
208
views
create genewise sync file in popoolation
popoolation
updated 5 days ago by 141k • written 5 days ago by • 0
0
votes
2
replies
529
views
How to get the reference panel for UKBB
UKBB GWAS clump
5 days ago by 航太郎 • 0
286 results • Page 4 of 6
Recent Votes
Comment: some error in building kraken2 database
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
C: RSeQC Output from infer_experiment.py - what does it mean?
Read pair orientation : Illumina TruSeq Stranded mRNA library
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
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Recent Replies
Comment: Use of Kraken output for functional analysis by gv • 0
Hello, you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport cheers,
Answer: To get p-values for the TPM by VITALA • 0
sir, deseq2 takes counts as inputs na for the hypothesis testing /to see the variance between the two groups, but in my case what i want is…
Answer: To get p-values for the TPM by dsull ★ 5.8k
There are plenty of RSEM -> tximport -> DESeq2 tutorials online. Just follow one of those. DESeq2 will give you "p values" based on a Wa…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by dsull ★ 5.8k
I agree for the most part. However, Heng Li has argued that the one application that they are essential for is short read variant calling. …
Comment: interpretartion of a vcf file by samuelkalandarov2002 ▴ 10
In my case , there is only one sample : here is an example of a some variants generated using minipileup : #CHROM POS ID REF ALT QUAL FI…
Comment: How to calculate identity percentage between proteins contained in a FASTA file? by b.contreras.moreira ▴ 170
This should work if you know your sequences are related and can be globally aligned; otherwise it is safer to compute local alignments (for…
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…
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