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85
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 18 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 2 hours ago by • 0 • written 12.0 years ago by ★ 2.9k
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 2 hours ago by 43k • written 4.5 years ago by ★ 1.4k
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 6 hours ago by 6.3k • written 10.9 years ago by ▴ 10
9
votes
3
replies
6.9k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq edgeR Batch-Effect
updated 2 hours ago by 43k • written 9.9 years ago by ▴ 250
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 2 hours ago by 43k • written 4.5 years ago by ▴ 140
8
votes
6
replies
2.5k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 22 hours ago by 3.0k • written 23 months ago by ▴ 230
7
votes
5
replies
3.6k
views
ISCN annotation for SV/CN VCF files
SV
updated 16 hours ago by • 0 • written 7 months ago by ▴ 50
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 2 hours ago by 43k • written 7.0 years ago by ▴ 80
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat RNA-Seq Limma DESeq2 batch-effect
updated 2 hours ago by 43k • written 4.9 years ago by ▴ 140
5
votes
4
replies
412
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq EdgeR DEGs DESeq2
58 minutes ago by BioinfGuru ★ 1.7k
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 2 hours ago by 43k • written 9.1 years ago by ▴ 110
4
votes
2
replies
3.7k
views
DESeq2 design and batch effect
RNA-Seq batch-effect DESeq2 Salmon
updated 2 hours ago by 43k • written 6.5 years ago by ▴ 30
4
votes
2
replies
211
views
Assume "yes" as the answer to any prompts with bioconda
docker container bioconda
updated 9 hours ago by 8.5k • written 10 hours ago by ▴ 20
3
votes
1
reply
549
views
What is the normalization status of metabric data?
metabric normalization microarray cbioportal
updated 20 hours ago by ▴ 20 • written 19 months ago by ★ 4.3k
3
votes
3
replies
2.9k
views
Quick way to Identify batch effect from covariates?
bioconductor batch-effect
updated 2 hours ago by 43k • written 7.9 years ago by ★ 3.4k
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 2 hours ago by 43k • written 7.1 years ago by ▴ 310
3
votes
2
replies
4.1k
views
Batch effects in sequencing data
batch-effect
updated 2 hours 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 2 hours ago by 43k • written 4.5 years ago by ▴ 180
3
votes
4
replies
314
views
biomaRt error for different R version
biomaRt R
updated 8 hours ago by 141k • written 1 day ago by ▴ 490
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray batch-effect
updated 2 hours ago by 43k • written 9.6 years ago by • 0
2
votes
10
replies
538
views
Questions about a bug when transferring cram file to bam file
sequence samtools bcftools
updated 5 hours ago by 141k • written 1 day ago by • 0
2
votes
2
replies
315
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression edgeR
4 hours ago by nhaus ▴ 300
2
votes
2
replies
245
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
updated 4 hours ago by ★ 1.2k • written 12 hours ago by ▴ 30
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq batch-effect sequencing
updated 2 hours ago by 43k • written 6.9 years ago by • 0
2
votes
2
replies
1.8k
views
Time point microarray data correcting for batch effects
microarray combat batch-effect
updated 2 hours ago by 43k • written 6.7 years ago by ▴ 10
2
votes
1
reply
2.3k
views
TCGA RNAseqV2 data matrix batch effect control and remove
RNA-Seq batch-effect
updated 2 hours ago by 43k • written 7.6 years ago by ▴ 10
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 2 hours ago by 43k • written 7.6 years ago by ▴ 70
2
votes
6
replies
565
views
Removing duplicates
duplicates ONT minimap2
12 hours ago by quentinperriere • 0
2
votes
2
replies
1.1k
views
Can we directly use batch corrected gene expression (Bulk RNA-seq) for further downstream analyses?
RNA-Seq batch-effect
updated 2 hours ago by 43k • written 5.0 years ago by ▴ 60
2
votes
3
replies
309
views
Sheep reference genome remapping coordinates
reference remap sheep coordinates genome
8 hours ago by valentinatsar • 0
2
votes
2
replies
1.0k
views
Batch correct batch 2 while leaving batch 1 unchanged.
limma machine-learning batch-effect
updated 2 hours ago by 43k • written 3.7 years ago by 19k
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 2 hours ago by 43k • written 3.5 years ago by ▴ 20
2
votes
6
replies
5.1k
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 2 hours ago by 43k • written 3.7 years ago by • 0
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 6 hours ago by 43k • written 4.8 years ago by ▴ 20
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray combat batch-effect median-normalization
updated 2 hours ago by 43k • written 17 months 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 2 hours ago by 43k • written 7.2 years ago by ▴ 20
1
vote
3
replies
106
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated just now by 43k • written 4 hours ago by • 0
1
vote
1
reply
178
views
Pediococcus acidilactici sequence analysis
BLAST Gene-Ontology
updated 15 hours ago by 43k • written 21 hours ago by ▴ 120
1
vote
9
replies
1.1k
views
Supergnova stuck in tutorial
Genetic Correlations Python Supergnova Conda
updated 10 hours ago by • 0 • written 19 months ago by ▴ 10
1
vote
4
replies
317
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
updated 8 hours ago by 141k • written 12 hours ago by • 0
1
vote
2
replies
216
views
Korean human genome reference file
GWAS reference imputation
updated 8 hours ago by 141k • written 12 hours ago by • 0
1
vote
9
replies
558
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 7 hours ago by ★ 2.4k • written 12 hours ago by • 0
1
vote
4
replies
549
views
What happened to Tombo Re-squiggle
Tombo resquiggle ONT
updated 5 hours ago by 43k • written 3 months ago by • 0
1
vote
1
reply
194
views
Problem with Mirdeep2 and Randfold output
mirdeep2 Randfold
5 hours ago by otieno43 ▴ 30
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS exome-sequencing batch-effect
updated 2 hours ago by 43k • written 6.5 years ago by ▴ 270
1
vote
2
replies
2.9k
views
Taking surrogate variable into account before running PCA
sva svaseq batch-effect
updated 2 hours ago by 43k • written 6.8 years ago by • 0
1
vote
3
replies
2.0k
views
gene expression data analysis and batch effect methods
microarray Gene-expression batch-effect
updated 2 hours ago by 43k • written 6.9 years ago by ▴ 220
1
vote
4
replies
3.1k
views
remove batch effect for multiple tumor data
RNA-Seq batch-effect
updated 2 hours ago by 43k • written 7.1 years ago by ▴ 40
1
vote
4
replies
1.4k
views
Removing/Accounting for batch effects in unbalanced group RNAseq data
rna-seq batch-effect deseq
updated 2 hours ago by 43k • written 2.2 years ago by • 0
99 results • Page 1 of 2
Recent Votes
Answer: Bedtools nuc : calculating the GC content in a sliding window
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
Comment: Questions about a bug when transferring cram file to bam file
A: Out Of Disk Space With Picard Tools ?
Exporting WGCNA step-to-step network construction objects into igraph object
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Recent Replies
Comment: Downloaded pdb's on rcsb.org by Ram 43k
PDB has a search API: https://search.rcsb.org/#search-example-1 Here's the JSON from your search query: ``` { "query": { "type": "grou…
Comment: Downloaded pdb's on rcsb.org by iamsmor • 0
Thank you very much. Actually I looked at there, but actually I want to find something like according to search url like this [QUERY: Gene …
Comment: DEG analysis of RNA-seq data across multiple tissues and two conditions by BioinfGuru ★ 1.7k
great guidance ... thank you
Comment: error in CPC2 by Ram 43k
Ashok, what is CPC2? Please edit your post and add as much context as you can.
Comment: python file for cpc2 by Ram 43k
Ashok - someone else had to (guess and) add context to your post. Please give us as much information as you can in the first place - we can…
Comment: python file for cpc2 by Pierre Lindenbaum 161k
https://academic.oup.com/nar/article/45/W1/W12/3831091 > CPC2: a fast and accurate coding potential calculator based on sequence intrinsic…
Comment: error in CPC2 by GenoMax 141k
Looks like you are running code that was written for `python v.2.x` but you probably have `python v.3.x` or a newer version than `python v.…
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.
Answer: 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 …
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