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450 results • Page 5 of 9
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166
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Identification of Transgene insertion sites
Transgene Whole-Genome-Sequencing transgene-sites
updated 15 days ago by 43k • written 15 days ago by • 0
0
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1
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1.8k
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Advice required for remove batch effect which perfectly collinear with contrast of interest
RNA-seq batch-effect
updated 19 days ago by 43k • written 6.7 years ago by ▴ 80
0
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1
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194
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Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 14 days ago by ★ 2.4k • written 14 days ago by • 0
0
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1
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179
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 13 days ago by ★ 27k • written 14 days ago by • 0
0
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1
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285
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cibersort. problem
cibersort gema122
updated 29 days ago by 43k • written 4 weeks ago by • 0
0
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1
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177
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Problem with Seurat package in PercentageFeatureSet function
cell single
updated 1 day ago by ★ 2.4k • written 2 days ago by ▴ 60
1
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1
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248
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Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing housekeeping Single-cell normalization
updated 12 days ago by 82k • written 12 days ago by • 0
1
vote
1
reply
1.7k
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sea corrected expression matrix
sva microarrays batch-effect
updated 20 days ago by 43k • written 6.8 years ago by ▴ 380
1
vote
1
reply
184
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Failed to download data from EBI with ascp
EBI aspera
updated 26 days ago by 142k • written 26 days ago by ▴ 60
0
votes
1
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70
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Correlating Bulk Differential Expression with quantitative
Differential-Expression DESeq2
updated 44 minutes ago by 43k • written 5 hours ago by • 0
0
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1
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189
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Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 6 days ago by 19k • written 7 days ago by • 0
1
vote
1
reply
200
views
Help/Direction Needed for Data Analysis of RNA
Sequencing RNA-seq DNA-Seq
updated 21 days ago by ★ 6.0k • written 21 days ago by • 0
0
votes
1
reply
195
views
Extract Di-nucleotide/Tri-Nucleotide substitution frequencies from MSA/VCF file
MSA substitution VCFstats Evolution VCF
updated 27 days ago by 161k • written 27 days ago by ▴ 50
0
votes
1
reply
175
views
unable to get feature count results
featureCounts
updated 7 days ago by 43k • written 7 days ago by • 0
0
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1
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829
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR Batch-effect RNA-Seq
updated 19 days ago by 43k • written 3.7 years ago by • 0
0
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1
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230
views
Extracting mutation status from MAF files - TCGA
TCGA maf mutation
updated 3 days ago by • 0 • written 4 days ago by • 0
0
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1
reply
836
views
How to compare differentially expressed genes among different affymatrix dataset
microarray batch-effect R
updated 20 days ago by 43k • written 4.8 years ago by ▴ 30
0
votes
1
reply
295
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 20 days ago by 142k • written 20 days ago by • 0
0
votes
1
reply
231
views
merging Seurat objects after SCT
Seurat SCT
updated 22 days ago by 43k • written 22 days ago by • 0
0
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1
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684
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 6 days ago by 43k • written 7 days ago by • 0
1
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1
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259
views
RNA seq normalization and gene gene correlation
rna-seq pearson-correlation vst
updated 25 days ago by 43k • written 25 days ago by • 0
1
vote
1
reply
443
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA Limma
updated 17 days ago by ★ 7.1k • written 19 days ago by ▴ 280
0
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1
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208
views
Help with DGEList function
DGEList R
updated 2 days ago by ▴ 90 • written 3 days ago by • 0
0
votes
1
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93
views
Differentail gene expression results
differential expression gene rna-seq Deseq2
updated 13 hours ago by 82k • written 14 hours ago by • 0
0
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1
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220
views
Annotating a dataset with gnomAD v4 using Hail
Python Sequencing Hail Exome Annotation
updated 20 days ago by ▴ 40 • written 20 days ago by • 0
0
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1
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219
views
Pattern of GC content across reads from fastp
multiqc ddRAD
updated 29 days ago by 142k • written 29 days ago by • 0
0
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1
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181
views
P-values for pairwise FST
FST P-value pairwise
updated 28 days ago by ★ 1.9k • written 28 days ago by ▴ 50
0
votes
1
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309
views
Could you please assist in identifying this cluster?
single-cell
updated 18 days ago by 43k • written 18 days ago by ▴ 30
0
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1
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154
views
tbtool
tbtool
updated 15 days ago by 43k • written 15 days ago by • 0
0
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1
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255
views
Two databases: Human Microbiome Project and MGnify
Microbiome databases
updated 22 days ago by 142k • written 22 days ago by ▴ 360
1
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1
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249
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Retrieve a % coverage for each transcript
RNA-seq
updated 20 days ago by 43k • written 20 days ago by ▴ 40
0
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1
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555
views
Differential Expression Analysis for miRNA
limma Differential-gene-Expression miRNA
updated 28 days ago by 43k • written 3.0 years ago by • 0
0
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1
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1.1k
views
Ensembl assembly choice for RNA-Seq reference mapping
RNA-Seq ensembl STAR alignment Assembly
updated 26 days ago by ▴ 20 • written 5.0 years ago by ▴ 30
0
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1
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274
views
How to do further funtional analysis of DEG KeggGet output list?
KEGGREST DESEQ2 RNA-Seq DEG
29 days ago by joana.maclean • 0
1
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1
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206
views
ComplexHeatmap anno_mark position changes with height of gene expression heatmap
ComplexHeatmap
22 days ago by CTLong ▴ 110
1
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1
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2.7k
views
Plotting a PCA Plot from SVASeq results
pca ruvseq sva svaseq batch-effect
updated 20 days ago by 43k • written 6.3 years ago by ▴ 40
0
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1
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1.2k
views
Controlling for batch effect in SNP-based PCA
whole-genome PCA batch-effect SNP
updated 20 days ago by 43k • written 4.7 years ago by ▴ 90
0
votes
1
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244
views
Design matrix after RUVg correction
limma ruvseq differential-expression
updated 28 days ago by 43k • written 3 months ago by ▴ 10
1
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1
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112
views
student
epitranscriptomics
updated 14 hours ago by 82k • written 15 hours ago by • 0
0
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1
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190
views
Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 14 days ago by ★ 2.4k • written 14 days ago by ▴ 110
0
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1
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1.2k
views
Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
random-effects RNA-Seq batch-effect
updated 20 days ago by 43k • written 6.8 years ago by • 0
0
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1
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147
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome 16S DESeq2
updated 15 hours ago by 3.6k • written 1 day ago by • 0
0
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1
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190
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
updated 13 days ago by • 0 • written 13 days ago by • 0
0
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1
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216
views
Finding batch and outlayers
Pca
updated 8 days ago by ▴ 460 • written 9 days ago by • 0
0
votes
1
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184
views
Differential Accessibility
DiffBind
updated 8 days ago by 43k • written 8 days ago by • 0
0
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1
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188
views
filtering before dada2
bbduk qiime2 dada2 metagenomic
updated 3 days ago by 43k • written 4 days ago by • 0
0
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1
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310
views
Sheep-Human ortholog mapping with BioMart and Orthogene/Gprofiler
ortholog sheep
updated 29 days ago by • 0 • written 4 months ago by • 0
0
votes
1
reply
588
views
Basic stats in hierfstat
Fst stats hierfstat
updated 6 days ago by • 0 • written 18 months ago by • 0
3
votes
1
reply
281
views
how to change the gene header names in a fasta file?
fasta bioawk awk seqkit
updated 25 days ago by 43k • written 26 days ago by • 0
1
vote
1
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99
views
Gene density plot
density gene
updated 10 hours ago by ★ 1.9k • written 16 hours ago by ▴ 290
450 results • Page 5 of 9
Recent Votes
A: Download full list of SNPs and their coordinates in hg38
Answer: HCL database download
Answer: Tissue-specific DEG analysis with DEseq2
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Comment: How to access TCGA samples that were treated with a specific drug?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
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Recent Replies
Answer: HCL database download by sooni ▴ 20
I solved the problem by conneting another internet exploer. I think it was probably a problem with Chrome itself.
Answer: barcode of TCR-sequencing by mizraelson ▴ 60
Hi, What protocol did you use for TCR-seq library preparation? Generally speaking, there is no need to remove barcodes, as MiXCR can work …
Comment: Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, C by qwertyuiop26 • 0
I've implemented fm index with backward search and need an inexact search to implement on FM index, I couldn't understand how fm index coul…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by Chris Dean ▴ 400
The md5 hash they refer to on line 22 (f46a7ca244afef522b22a11bd33d27b1) appears to map to a *S. aureus* strain, not *S. hominis* (you can …
Comment: Correlating Bulk Differential Expression with quantitative by Qroid ▴ 40
You could try including disease scale for each sample as a design factor. See the vignette here https://bioconductor.org/packages/devel/bio…
Comment: Help with generating annotation database for dog genome to use in ANNOVAR for v by sainavyav22 • 0
Hello, Thanks for the reply. I could only see the refMrna.fa file in the link you provided. Where can I get the refGene.txt file. Thanks fo…
Answer: Understanding STAR output (Aligned.out.sam file) by heelpPlease • 0
After thoroughly reviewing all the documents again, I've identified the root cause of my initial issue: the failure to detect essential gen…
Comment: Understanding STAR output (Aligned.out.sam file) by heelpPlease • 0
Thank you! Now that I understand that there is a difference between read and fragment, I could actually find a lot of helpful information..…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 90
Thanks again. Hmm...this makes me suspicious of whether this normalization is actually possible. In case you'd like to take a look, [here]…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Jeremy Leipzig 22k
The seven genotypes being 58025AA, 58025AG, 58051TT, 58051TC, 58051CC, 58057TT, 58057TC
Answer: TFs and Gene databases by jared.andrews07 ★ 16k
See [TFlink](https://tflink.net/), [KnockTF2](https://bio.liclab.net/KnockTFv2/index.php), [TFBSDB](https://tfbsdb.systemsbiology.net/), an…
Comment: Filtering Multi-sample VCF file for all except one Genotype by GenoMax 142k
> Seven genotpyes have been sampled and all variants, which belong to one of those genotpyes are to be "erased" (or every other variant exc…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Pierre Lindenbaum 161k
> , filter a multisample VCF file for all genotypes except one of them filter for what ?
Answer: Applying the metacell2 algorithm using python by Wayne ★ 2.0k
I had hoped things like [this Jupyter notebook for the rabbit data analysis](https://nbviewer.org/github/tanaylab/rabembflow/blob/master/2-…
Comment: Help with running egsea() by 1769mkc ★ 1.2k
please provide the design matrix mean the metadata of the model fit2 which is there in the code . i guess other users can help
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