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54
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12
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28k
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12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 5 days ago by • 0 • written 12.0 years ago by ★ 2.9k
87
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 6 days ago by • 0 • written 3.5 years ago by 3.2k
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read length bam
updated 5 days ago by ▴ 10 • written 10.2 years ago by ▴ 180
76
votes
71
replies
19k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 1 day ago by 141k • written 6.2 years ago by 87k
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 5 days ago by 6.4k • written 10.9 years ago by ▴ 10
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
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 2 days ago by 43k • written 10.6 years ago by ▴ 150
23
votes
23
replies
9.8k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq removeBatchEffect batch-effect edger
updated 6 days ago by 43k • written 5.3 years ago by ▴ 130
9
votes
3
replies
6.9k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq edgeR Batch-Effect
updated 5 days ago by 43k • written 9.9 years ago by ▴ 250
11
votes
9
replies
6.9k
views
How to choose method to integrate different patient sample together in Seurat
Seurat scRNA batch-effect harmony
updated 6 days ago by 43k • written 4.2 years ago by ▴ 80
9
votes
10
replies
6.9k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat scRNA-seq Harmony RNA-seq batch-effect
updated 5 days ago by 43k • written 4.5 years ago by ▴ 140
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 5 days ago by 43k • written 4.6 years ago by ★ 1.4k
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
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 4 days ago by • 0 • written 6.5 years ago by ▴ 30
2
votes
7
replies
5.2k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated 4 days ago by 82k • written 7.1 years ago by ▴ 80
2
votes
6
replies
5.2k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq R seurat harmony batch-effect
updated 5 days ago by 43k • written 3.7 years ago by • 0
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray batch-effect
updated 5 days ago by 43k • written 9.7 years ago by • 0
8
votes
5
replies
4.8k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by ▴ 60
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
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
3
votes
2
replies
4.1k
views
Batch effects in sequencing data
batch-effect
updated 5 days ago by 43k • written 8.7 years ago by ▴ 60
3
votes
8
replies
4.1k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm scRNA-seq RNA-Seq tpm batch-effect
updated 5 days ago by 43k • written 4.6 years ago by ▴ 180
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
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq deseq2 batch-effect
updated 6 days ago by 43k • written 4.9 years ago by ▴ 330
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq batch-effect
updated 6 days ago by 43k • written 4.8 years ago by ▴ 30
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq batch-effect DESeq2 Salmon
updated 5 days ago by 43k • written 6.5 years ago by ▴ 30
25
votes
11
replies
3.7k
views
6 follow
Forum: Site Use Guidelines
meta biostars Guidelines
updated 15 hours ago by 43k • written 14.6 years ago by 100k
1
vote
3
replies
3.6k
views
Does Harmony batch correction for scRNA-seq require the same populations to be present in all samples?
Harmony single-cell scRNA-seq batch-effect
updated 5 days ago by 43k • written 4.5 years ago by ▴ 140
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
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence RNA-Seq RPKM Fold-Change batch-effect
updated 6 days ago by 43k • written 7.0 years ago by ▴ 20
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
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
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
2
votes
1
reply
3.1k
views
Batch effect correction in DE analysis of single cell RNA-seq data and visualization
Seurat Batch-effect SCDE RNA-Seq Limma
updated 6 days ago by 43k • written 5.5 years ago by ▴ 60
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
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
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor batch-effect
updated 5 days ago by 43k • written 7.9 years ago by ★ 3.4k
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
1
vote
2
replies
2.9k
views
Taking surrogate variable into account before running PCA
sva svaseq batch-effect
updated 5 days ago by 43k • written 6.9 years ago by • 0
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
7
votes
3
replies
2.8k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 5 days ago by 6.4k • written 15 months ago by ▴ 130
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
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
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
4
votes
9
replies
2.6k
views
Tool: CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by • 0
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 5 days ago by 43k • written 9.1 years ago by ▴ 110
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
6
votes
0
replies
2.6k
views
Tool: Immuno-Navigator, a batch-corrected database for gene coexpression in the immune system
gene-co-expression batch-effect immunology
updated 5 days ago by 43k • written 7.0 years ago by ▴ 80
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 6 days ago by 3.0k • written 23 months ago by ▴ 230
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
285 results • Page 1 of 6
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Answer: To get p-values for the TPM
Comment: To get p-values for the TPM
A: Finding the centromere and telomere of cattle genome (Bos Taurus)
A: How to systematically check if a bam file is truncated
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?
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Comment: To get p-values for the TPM by ATpoint 82k
Seconding that. Just use established pipelines, tximport => DESeq2, get your stats and call it a day. Custom pipelines paired with little e…
Comment: Should I remove unlocalized scaffols in reference genome before alignment? by njornet ▴ 20
I don't want reads incorrectly aligned to these scaffolds and loose information of relevant regions, but as you said that probably won't ha…
Comment: To get p-values for the TPM by dsull ★ 5.8k
Your post should be a "com, not an "answer". Use "Add Comment" to request clarifications on an answer someone has provided. tximport can t…
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,
Comment: To get p-values for the TPM by VITALA • 0
sir, deseq2 takes counts as inputs rightfor the hypothesis testing /to see the variance between the two groups, but in my case what i want …
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…
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