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975 results • Page 6 of 20
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4
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1.2k
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Batch effects
Batch-effect transcriptomics
updated 18 days ago by 43k • written 2.6 years ago by ▴ 30
11
votes
11
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1.2k
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7 follow
How I know if it is a batch effect or are real differences between my controls and treatments?
RNA-seq Transcriptomics ComBat-seq Batch-Effect
updated 27 days ago by 142k • written 4 weeks ago by ▴ 10
0
votes
1
reply
1.2k
views
Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
random-effects RNA-Seq batch-effect
updated 19 days ago by 43k • written 6.8 years ago by • 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 43k • written 4.7 years ago by ▴ 90
0
votes
9
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1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling single-cell scRNA-seq batch-effect
updated 19 days ago by 43k • written 3.9 years ago by ▴ 20
0
votes
0
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1.2k
views
Batch estimate using kBET
batch-effect kbet
updated 18 days ago by 43k • written 4.1 years ago by • 0
0
votes
5
replies
1.2k
views
RNAseq differential gene expression analysis yield results which come from digestive content
differential-gene-expression RNA-Seq
updated 27 days ago by 43k • written 6.4 years ago by ▴ 90
0
votes
0
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1.2k
views
Extra adjustment variables during batch effect correction
rna-seq ComBat batch-effect
updated 19 days ago by 43k • written 4.3 years ago by ▴ 360
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
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva combat batch-effect SNP
updated 21 days ago by 43k • written 4.2 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Ensembl assembly choice for RNA-Seq reference mapping
RNA-Seq ensembl STAR alignment Assembly
updated 25 days ago by ▴ 20 • written 5.0 years ago by ▴ 30
0
votes
0
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1.1k
views
Should batch correction be performed before or after feature selection in scRNA-seq
batch-effect scRNA-seq feature-selection
updated 19 days ago by 43k • written 5.0 years ago by ▴ 140
2
votes
2
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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
1
vote
2
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1.1k
views
News: The GDC Legacy Archive is retiring soon.
genomic-data-commons tcga gdc
1 day ago by Zhenyu Zhang ★ 1.2k
3
votes
0
replies
1.1k
views
Tool: Sars-Cov-2 Genome & ACE 2 Exploration
sequence alignment SNP genome
1 day ago by Ibrahim Tanyalcin ★ 1.2k
2
votes
2
replies
1.1k
views
DESeq2 for Differential gene expression
differential-gene-expression
updated 27 days ago by 43k • written 3.8 years ago by ▴ 10
0
votes
16
replies
1.1k
views
What is the sequence origin in human plasma?
human sequence cfDNA
23 days ago by biwdpang • 0
0
votes
3
replies
1.1k
views
Discrepancy between E() Values in Blastp Search - HELP
BLAST E-value Blastp Protein
updated 19 days ago by 43k • written 5.3 years ago by • 0
11
votes
12
replies
1.1k
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated 18 days ago by 43k • written 18 days ago by • 0
0
votes
0
replies
1.1k
views
Finding wobble/redundant positions in an RNA string using R.
RNA wobble-position R
updated 19 days ago by 43k • written 6.2 years ago by ▴ 100
8
votes
16
replies
1.1k
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 10 days ago by ★ 2.4k • written 8 weeks ago by • 0
7
votes
7
replies
1.1k
views
Prediction tools summary - zero values
statistics
updated 20 days ago by • 0 • written 6 months ago by ▴ 50
0
votes
0
replies
1.1k
views
Isoforms or Duplications
Differential-Gene-Expression RNA-Seq
updated 27 days ago by 43k • written 7.1 years ago by ▴ 10
1
vote
0
replies
1.1k
views
interpretation of trajectory and batch effect
monocle3 batch-effect trajectory
updated 28 days ago by 43k • written 3.5 years ago by ▴ 10
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado filtering QC nanopore Guppy
4 days ago by eebloom ▴ 80
5
votes
2
replies
1.1k
views
How to perform batch correction when we have only single condition?
sva combat batch-effect DESeq2
updated 20 days ago by 43k • written 3.8 years ago by ▴ 680
1
vote
3
replies
1.0k
views
problem with facing strange gene name in TCGA data
TCGA RNA-Seq batch-effect
updated 19 days ago by 43k • written 5.7 years ago by ▴ 170
0
votes
6
replies
1.0k
views
Considering that the basal expression level is not 0 for the calculation of the differential expression
DESEQ2 RNA-Seq Differential-gene-Expression
updated 27 days ago by 43k • written 5.8 years ago by ▴ 340
5
votes
14
replies
1.0k
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications dorado basecalling nanopore methylation
updated 25 days ago by 142k • written 6 weeks ago by ▴ 20
2
votes
2
replies
1.0k
views
Batch correct batch 2 while leaving batch 1 unchanged.
limma machine-learning batch-effect
updated 18 days ago by 43k • written 3.8 years ago by 19k
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat RNA-Seq batch-effect
updated 19 days ago by 43k • written 4.3 years ago by ▴ 360
0
votes
2
replies
1.0k
views
proportional hazard assumption was not satisfied for a covariate
hazard-ratios Cox-model survival
updated 19 days ago by 43k • written 4.4 years ago by ▴ 40
3
votes
2
replies
1.0k
views
Can I take 'organ type' as a batch effect and use ComBat to remove organ dependent variations?
RNA-Seq Cross-Species SVA ComBat Batch-Effect
updated 19 days ago by 43k • written 4.7 years ago by • 0
2
votes
5
replies
1.0k
views
Ties in reranked list
fgsea GSEA
updated 23 days ago by • 0 • written 7 months ago by • 0
1
vote
10
replies
1.0k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq DESeq2 DNA-contamination
12 days ago by DKA ▴ 40
2
votes
3
replies
989
views
Treating "patient" as a batch effect
ComBat_seq DESeq2 batch-Effect
updated 20 days ago by 43k • written 17 months ago by ▴ 20
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
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
4
votes
13
replies
955
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 19 days ago by ★ 1.7k • written 25 days 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 19 days ago by 43k • written 4.6 years ago by ▴ 40
1
vote
1
reply
942
views
Easiest way to Get gene Id's from Affymetrix Probeset id's
microarray differential-gene-expression r
updated 27 days ago by 43k • written 5.5 years ago by ▴ 40
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
5
replies
931
views
Retrieval of Active site information programmatically
Catalytic Python Active PDB site Site
updated 7 days ago by ★ 2.0k • written 2.0 years ago by • 0
2
votes
11
replies
919
views
Questions about a bug when transferring cram file to bam file
sequence samtools bcftools
updated 7 days ago by ★ 1.2k • written 19 days ago by • 0
2
votes
9
replies
914
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 12 days ago by 4.2k • written 6 months ago by • 0
1
vote
8
replies
908
views
Adding CB tag to bam file
samtools bam
updated 11 days ago by 161k • written 18 days ago by • 0
2
votes
7
replies
908
views
Removing duplicates
duplicates ONT minimap2
updated 17 days ago by ▴ 580 • written 19 days ago by • 0
3
votes
6
replies
902
views
Any problem re-using last year's RNA-Seq data in this year's analysis?
RNA-Seq batch-effect
updated 19 days ago by 43k • written 3.7 years ago by ▴ 20
1
vote
1
reply
900
views
Any strategies to compare gene and protein expression dataset and perform differential expression
gene-expression R protein-expression Differential-gene-expression Volcano-plot
updated 27 days ago by 43k • written 2.3 years ago by ▴ 10
3
votes
9
replies
897
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 18 days ago by ★ 2.4k • written 18 days ago by • 0
975 results • Page 6 of 20
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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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