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369 results • Page 1 of 8
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85
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 16 hours ago by • 0 • written 3.5 years ago by 3.2k
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 40 minutes ago by • 0 • written 12.0 years ago by ★ 2.9k
39
votes
9
replies
42k
views
6 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 1 day ago by 43k • written 6.7 years ago by ★ 1.3k
30
votes
12
replies
3.8k
views
Trying to understand the maths behind one Limma function
limma RNA-Seq batch-effect
updated 3 days ago by 43k • written 4.0 years ago by ▴ 330
23
votes
11
replies
4.8k
views
7 follow
Code golf: detecting homopolymers of length N in the (human) genome
code golf fasta homopolymer repeat
updated 2 days ago by 43k • written 4.9 years ago by 47k
23
votes
23
replies
9.7k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq removeBatchEffect batch-effect edger
updated 1 day ago by 43k • written 5.3 years ago by ▴ 130
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 24 minutes ago by 43k • written 4.5 years ago by ★ 1.4k
15
votes
6
replies
1.2k
views
6 follow
VCF to human friendly form?
vcf visualization
updated 3 days ago by 161k • written 19 months ago by ▴ 10
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 1 day ago by 43k • written 6.8 years ago by ★ 1.3k
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 1 day ago by 43k • written 4.2 years ago by ▴ 80
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly statistics
updated 5 days ago by • 0 • written 4.7 years ago by ▴ 10
10
votes
7
replies
7.0k
views
6 follow
Convert GVF to VCF
vcf
updated 2 days ago by • 0 • written 9.2 years ago by ▴ 970
10
votes
36
replies
5.7k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA batch-effect DESeq2 R
updated 1 day ago by 43k • written 5.7 years ago by ▴ 620
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 4 hours ago by 6.3k • written 10.9 years ago by ▴ 10
9
votes
10
replies
6.8k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat scRNA-seq Harmony RNA-seq batch-effect
updated 20 minutes ago by 43k • written 4.5 years ago by ▴ 140
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq batch-effect
updated 1 day ago by 43k • written 7.3 years ago by ▴ 30
9
votes
3
replies
6.9k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq edgeR Batch-Effect
updated 25 minutes ago by 43k • written 9.9 years ago by ▴ 250
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq deseq2 batch-effect
updated 1 day ago by 43k • written 4.9 years ago by ▴ 330
9
votes
4
replies
1.9k
views
Integration of RNA-Seq data with microarray data
microarray RNA-Seq batch-effect R
updated 1 day ago by 43k • written 4.0 years ago by ▴ 30
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl repeat
updated 3 days ago by ▴ 190 • written 15 months ago by ★ 1.4k
8
votes
10
replies
649
views
bash script
whole-genome-sequencing
updated 2 days ago by 43k • written 10 days ago by ▴ 30
8
votes
6
replies
2.5k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 20 hours ago by 3.0k • written 23 months ago by ▴ 230
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression TPM RNA-Seq counts batch-effect
1 day ago by Ram 43k
7
votes
7
replies
516
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein pdb protein-databank
updated 5 days ago by 4.5k • written 6 days ago by • 0
7
votes
4
replies
1.4k
views
Is there any journal article to reference removeBatchEffect function from Limma?
batch removebatcheffect limma rna-seq batch-effect
updated 1 day ago by 43k • written 21 months ago by ▴ 20
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt R
updated 1 day ago by 43k • written 3.8 years ago by ▴ 680
7
votes
8
replies
630
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter vcf coverage
updated 6 days ago by ▴ 40 • written 9 days ago by ▴ 40
7
votes
7
replies
805
views
Forum: Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career advice
updated 3 days ago by ★ 2.5k • written 3 days ago by • 0
7
votes
7
replies
1.0k
views
Prediction tools summary - zero values
statistics
updated 1 day ago by • 0 • written 6 months ago by ▴ 50
7
votes
2
replies
3.6k
views
Timeout on getBM() to retrieve snps from locations
biomaRt getBM R
updated 1 day ago by 43k • written 5.2 years ago by ▴ 600
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation RNA-Seq R
updated 1 day ago by 43k • written 6.0 years ago by ▴ 120
7
votes
5
replies
3.5k
views
ISCN annotation for SV/CN VCF files
SV
updated 14 hours ago by • 0 • written 7 months ago by ▴ 50
7
votes
3
replies
4.5k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA RNA-Seq batch-effect
updated 1 day ago by 43k • written 5.1 years ago by ▴ 100
7
votes
10
replies
2.6k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch batch-effect DESeq2 rna-seq
updated 1 day ago by 43k • written 24 months ago by ▴ 60
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray meta-analysis DEG batch-effect
updated 1 day ago by 43k • written 4.8 years ago by ▴ 30
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq edgeR DESeq2 Batch-Effect
updated 1 day ago by 43k • written 5.2 years ago by ▴ 40
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 1 day ago by • 0 • written 4.6 years ago by ▴ 40
6
votes
0
replies
2.5k
views
Tool: Immuno-Navigator, a batch-corrected database for gene coexpression in the immune system
gene-co-expression batch-effect immunology
updated 29 minutes ago by 43k • written 7.0 years ago by ▴ 80
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA gene-expression R
updated 1 day ago by 43k • written 5.2 years ago by ▴ 120
6
votes
8
replies
453
views
BRAKER3 genome annotation
annotation BRAKER3 genome
updated 1 day ago by 14k • written 3 days ago by ▴ 40
6
votes
17
replies
6.5k
views
Can you add a label key to heatscatter plot in R?
heatscatter visualization R
updated 1 day ago by 43k • written 9.5 years ago by ▴ 100
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq quantification alignment
updated 1 day ago by 43k • written 5.1 years ago by ▴ 250
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat RNA-Seq Limma DESeq2 batch-effect
updated 20 minutes ago by 43k • written 4.9 years ago by ▴ 140
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 1 day ago by 43k • written 4.7 years ago by ▴ 60
5
votes
5
replies
833
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq Blacklist
updated 6 days ago by 43k • written 10 months ago by ▴ 30
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov scatter-plot anova
updated 1 day ago by 43k • written 3.1 years ago by ▴ 170
5
votes
2
replies
1.0k
views
How to perform batch correction when we have only single condition?
sva combat batch-effect DESeq2
updated 1 day ago by 43k • written 3.7 years ago by ▴ 680
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq breast cancer subtyping
updated 1 day ago by ▴ 70 • written 5.6 years ago by ▴ 50
5
votes
5
replies
2.1k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq tophat batch-effect cufflinks
updated 1 day ago by 43k • written 5.3 years ago by • 0
5
votes
3
replies
298
views
Best genome browser for manual curation of gene structure(s)?
structure gene
updated 6 days ago by ★ 3.8k • written 7 days ago by ★ 5.3k
369 results • Page 1 of 8
Recent Votes
A: Out Of Disk Space With Picard Tools ?
Exporting WGCNA step-to-step network construction objects into igraph object
Comment: Downloaded pdb's on rcsb.org
Answer: How to compare the quality of assemblies
How to compare the quality of assemblies
A: Best strategy for gene annotation for de novo genome assembly without RNA-seq da
Comment: Questions about a bug when transferring cram file to bam file
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Commentator to GenoMax 141k
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Recent Replies
Comment: Per base sequence content failed miserably by GenoMax 141k
If this is 16S sequencing just follow the standard workflows like Qiime2.https://docs.qiime2.org/2024.2/tutorials/overview/
Comment: Out Of Disk Space With Picard Tools ? by kjngo • 0
Thanks changing the tmp dir fixed the out of disk space error for me as well.
Comment: Downloaded pdb's on rcsb.org by GenoMax 141k
Download services for PDB are described on this page: https://www.rcsb.org/docs/programmatic-access/file-download-services It could be as …
Answer: How to compare the quality of assemblies by shelkmike ★ 1.2k
Since BUSCO results are almost identical but the assembly sizes differ significantly, I suppose that the difference between the assemblies …
Comment: differential gene expression analysis when not all samples have an untreated cou by nhaus ▴ 300
Thank you very much for your answer, that was very helpful! > Impossible to say. It depends on your data, particularly on how the donors …
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues by bk11 ★ 2.3k
This could be because they are probably merging two or more datasets. If you are merging two or more datasets, it will be very important th…
Answer: Problem with Mirdeep2 and Randfold output by otieno43 ▴ 30
I sorted this out by first removing white space in the first line of the reference genome. Then indexed, the ran the mapper.pl script follo…
Comment: Questions about a bug when transferring cram file to bam file by GenoMax 141k
Just to be certain, you are saying that if OP runs `samtools view` without the explicit reference it will be automatically downloaded from …
Comment: Questions about a bug when transferring cram file to bam file by jkbonfield ★ 1.2k
That SQ M5 is chr1 in my copy of GRCh38 (Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa). I'm assuming your hg38.fa is not the sa…
Comment: What happened to Tombo Re-squiggle by Ram 43k
Please do not add answers unless you're answering the top level question. Instead, use `Add Comment` or `Add Reply` as appropriate. I've mo…
Comment: What happened to Tombo Re-squiggle by Joseph • 0
Hi, Does anybody has the answer to this? I also want to resquiggle my data with Remora but do not quite get which is the appropriate com…
Comment: How To Identify The 16S Rrna Gene Sequence In A Genome by colindaven 6.3k
It's also worth mentioning `Barrnap` is in the bacterial annotation system **Prokka**. `Prokka` can be installed on Debian systems with `…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by Elisabeth Gasteiger ★ 2.4k
See also https://www.uniprot.org/help/negative_datasets
Comment: Sheep reference genome remapping coordinates by valentinatsar • 0
Thank you for your response As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequen…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by me ▴ 750
Ok I made this into an answer. Could you please accept it as such.
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