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1,000 results • Page 5 of 20
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2
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2
replies
1.8k
views
Time point microarray data correcting for batch effects
microarray combat batch-effect
updated 7 days ago by 43k • written 6.7 years ago by ▴ 10
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat CNA Batch-Effect
updated 8 days ago by 43k • written 5.5 years ago by ▴ 150
3
votes
5
replies
1.8k
views
Limma/edgeR Design matrix for gender effect
RNA-Seq batch-effect
updated 8 days ago by 43k • written 4.7 years ago by • 0
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 7 days ago by 43k • written 6.6 years ago by ▴ 80
0
votes
5
replies
1.8k
views
Demultiplexing multiple amplicons from one fastq based on primer sequence
demultiplexing illumina
updated 16 days ago by 3.2k • written 3.4 years ago by • 0
2
votes
5
replies
1.8k
views
6 follow
DNA methylation preprocessing
Funnorm methylation Raw SWAN DNA
updated 24 days ago by • 0 • written 2.3 years ago by ▴ 10
1
vote
2
replies
1.8k
views
Data processing order: normalisation or batch effect correction first?
limma proteome batch-effect R
updated 8 days ago by 43k • written 3.5 years ago by ▴ 340
1
vote
0
replies
1.8k
views
Using SVA with RRBS data
sva batch-effect RRBS
updated 8 days ago by 43k • written 7.1 years ago by ▴ 50
0
votes
4
replies
1.8k
views
Correcting batch effect in unevenly distributed groups
RNA-Seq batch-effect R
updated 8 days ago by 43k • written 4.8 years ago by ▴ 20
2
votes
2
replies
1.8k
views
EdgeR in Galaxy. Adjust C-value?
Differential-gene-expression EdgeR Galaxy C-value
updated 16 days ago by 43k • written 7.6 years ago by ▴ 60
0
votes
0
replies
1.8k
views
Differential expression using Scran batch corrected data
single-cell Batch-effect RNA-Seq Scran
updated 7 days ago by 43k • written 5.5 years ago by ▴ 10
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF SAM BAM GFF minimap2
updated 8 days ago by ▴ 130 • written 12 months ago by • 0
0
votes
0
replies
1.7k
views
Accounting for hidden batch effects in differential expression analysis with DEXseq and Slueth
Batch-effect RNA-Seq Differential-Expression
updated 8 days ago by 43k • written 7.2 years ago by ▴ 270
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 8 days ago by 43k • written 2.9 years ago by ▴ 60
1
vote
3
replies
1.7k
views
Using Nanoplot to asses quality of ONT data
ONT Long-read-sequencing NanoPlot
updated 20 days ago by 43k • written 2.3 years ago by ▴ 10
1
vote
2
replies
1.7k
views
Batch effects and MDSPlot in limma
limma Batch-effect MDS Galaxy
updated 8 days ago by 43k • written 4.8 years ago by • 0
1
vote
1
reply
1.7k
views
sea corrected expression matrix
sva microarrays batch-effect
updated 8 days ago by 43k • written 6.8 years ago by ▴ 380
2
votes
2
replies
1.7k
views
Remove batch effect for many RNA-seq
ComBat RNA-Seq batch-effect sva
updated 8 days ago by 43k • written 4.8 years ago by • 0
1
vote
4
replies
1.7k
views
Batch correction and DE analysis of miRNA Seq data
miRNAseq Differential-Expression batch-effect
updated 7 days ago by 43k • written 5.1 years ago by ▴ 50
0
votes
0
replies
1.7k
views
Differential Gene Expression Analysis using two distinct scRNA-seq datasets
differential-gene-expression RNA-Seq scRNA-seq
updated 16 days ago by 43k • written 6.5 years ago by ▴ 120
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 8 days ago by 43k • written 4.7 years ago by ▴ 60
0
votes
0
replies
1.7k
views
Batch effect and CCA
CCA RNA-Seq seurat batch-effect
updated 8 days ago by 43k • written 5.1 years ago by ▴ 110
2
votes
2
replies
1.6k
views
How to add a title to a cnetplot?
r cnetplot
updated 8 days ago by 43k • written 3.5 years ago by ▴ 80
0
votes
5
replies
1.6k
views
what does mean this error ? "(ERR): hisat2-align exited with value 1" in mapping long noncoding RNAs
long-non-coding-RNA lncRNA
updated 20 days ago by 43k • written 2.6 years ago by • 0
2
votes
2
replies
1.6k
views
Combining control samples from 2 separate studies. Model matrix for batch effect?
gene-expression R limma batch-effect model-matrix
updated 7 days ago by 43k • written 7.2 years ago by ▴ 20
0
votes
1
reply
1.6k
views
RRBS data analysis using RnBeads give Scan() error
RRBS 450k RnBeads
updated 8 days ago by 43k • written 6.7 years ago by ▴ 40
0
votes
1
reply
1.6k
views
Public RNA-Seq and Microarray samples from same tissue
Microarray RNA-Seq Batch-Effect
updated 8 days ago by 43k • written 7.9 years ago by ★ 1.1k
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads RNA-seq gene-expression read-count
updated 20 days ago by 43k • written 2.9 years ago by • 0
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma sva batch-effect R
updated 10 days ago by 43k • written 3.8 years ago by ▴ 10
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome phg_v2 plants PHG
23 days ago by b.contreras.moreira ▴ 170
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat RNA-Seq Limma DESeq2 batch-effect
updated 7 days ago by 43k • written 4.9 years ago by ▴ 140
0
votes
1
reply
1.6k
views
Extraction of batch subject sequence from Blast result.
minus-strand blastdbcmd
updated 8 days ago by 43k • written 5.9 years ago by ▴ 80
2
votes
5
replies
1.6k
views
Adding functional annotation and meta-data of MAKER/BRAKER GFF
metadata functional-annotation BRAKER MAKER
updated 24 days ago by ▴ 40 • written 15 months ago by ▴ 60
5
votes
12
replies
1.5k
views
Subbmission Data
RNA-seq
updated 23 days ago by 43k • written 14 months ago by ▴ 50
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq edgeR DESeq2 Batch-Effect
updated 8 days ago by 43k • written 5.2 years ago by ▴ 40
4
votes
10
replies
1.5k
views
Do I have batch effect?
RNA-Seq edgeR batch-effect
updated 10 days ago by 43k • written 3.9 years ago by ▴ 20
3
votes
6
replies
1.5k
views
edgeR FDR always 1
FDR differential-gene-expression edgeR miRNA
updated 16 days ago by 43k • written 4.9 years ago by ▴ 20
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 16 days ago by 43k • written 4.9 years ago by • 0
9
votes
6
replies
1.5k
views
What in silico PCR commandline tool do you use that can handle IUPAC characters?
pcr amplicon primer
updated 23 days ago by 43k • written 16 months ago by ▴ 710
1
vote
5
replies
1.5k
views
How to correct unknown Batch effect?
PCA gene-expression DESeq2 RNA-seq batch-effect
updated 8 days ago by 43k • written 12 months ago by ▴ 110
0
votes
0
replies
1.5k
views
RIPSeeker viewRIP function fails to extract values() in GRangesList/S4 object
RIPSeq S4 RIP R
updated 8 days ago by 43k • written 6.2 years ago by ▴ 80
0
votes
0
replies
1.5k
views
minifi for RRBS
rrbs batch-effect methylation
updated 8 days ago by 43k • written 7.1 years ago by ★ 2.9k
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq quantification alignment
updated 8 days ago by 43k • written 5.1 years ago by ▴ 250
2
votes
3
replies
1.5k
views
RNASeq - How to compare the expression of a single gene across batches
RNA-Seq edgeR batch-effect
updated 7 days ago by 43k • written 3.5 years ago by ▴ 20
1
vote
5
replies
1.5k
views
Blastn in galaxy
Blastn galaxy
updated 23 days ago by 43k • written 3.0 years ago by • 0
0
votes
1
reply
1.4k
views
Assembled genome a little larger than Kmergeneie prediction?
kmergenie genome-size
updated 8 days ago by 43k • written 8.0 years ago by ▴ 40
4
votes
6
replies
1.4k
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3 GenomicRanges ORFik GenomicFeatures
updated 10 days ago by 141k • written 15 months ago by ▴ 30
0
votes
0
replies
1.4k
views
Help with Circos plot "Assumption Error" that prevents plotting a protein interactions network
CircosPlot
updated 8 days ago by 43k • written 3.3 years ago by • 0
1
vote
2
replies
1.4k
views
gdc-client command line error
line GDC TCGA command
updated 21 days ago by • 0 • written 20 months ago by • 0
10
votes
5
replies
1.4k
views
6 follow
Courses in RNAseq data
RNA-seq Courses
updated 23 days ago by 43k • written 2.5 years ago by ▴ 30
1,000 results • Page 5 of 20
Recent Votes
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
Detecting somatic variants in non-tumor tissue without normals
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
Comment: Why gatk VariantAnnotator required bam and coverage files
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
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Recent Replies
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Ram 43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Comment: Annovar using R package by DKA ▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis by ATpoint 82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets by ATpoint 82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
Comment: Why gatk VariantAnnotator required bam and coverage files by QX • 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis by kilcdincer ▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases by GenoMax 141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases by 5heikki 11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
Answer: why renaming Idents in Seurat object doesn't work? by Bioinfotec ▴ 10
I think when you give indent to seuObj : Idents(seuObj) <- 'RNA_snn_res.0.1' You may wrongly assign other value to it such as …
Answer: ScRNAseq-How to correctly choose cell type marker genes by Bioinfotec ▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question by Bioinfotec ▴ 10
In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification by GenoMax 141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing by rohitsatyam102 ▴ 850
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification by ATpoint 82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
Comment: Why gatk VariantAnnotator required bam and coverage files by Pierre Lindenbaum 161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
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