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331 results • Page 2 of 7
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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
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
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
4
votes
3
replies
2.2k
views
The result of differential gene expression analysis should be extracted based on adj.p.value ?
limma microarray bioconductor R
updated 6 days ago by 43k • written 6.3 years ago by ▴ 260
3
votes
2
replies
806
views
Retrieve initial query in getBM()
getBM biomaRt R gene
updated 6 days ago by 43k • written 3.2 years ago by • 0
3
votes
8
replies
1.2k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq Cellranger STARsolo 10X
updated 3 days ago by 14k • written 9 months ago by ▴ 80
3
votes
3
replies
455
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 3 days ago by 14k • written 4 days ago by ▴ 510
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
3
votes
3
replies
405
views
trouble using sequenceTubeMap in chromium installed on WSL
vg
6 days ago by ayushm64 • 0
3
votes
3
replies
493
views
Korean human genome reference file
GWAS reference imputation
4 days ago by SeoGyun • 0
3
votes
6
replies
8.3k
views
RNA-seq, EdgeR and batch effects
RNA-Seq removeBatchEffect edgeR batch-effect
updated 6 days ago by 43k • written 9.3 years ago by ▴ 120
3
votes
2
replies
2.1k
views
Batch effect correction - miRNA sequencing - DESeq2
Batch-effect DESeq2 miRNA-Seq
updated 6 days ago by 43k • written 5.5 years ago by • 0
3
votes
5
replies
2.1k
views
DE analysis with edgeR and possibly batch effect
analysis edgeR batch-effect DE
updated 6 days ago by 43k • written 5.1 years ago by ★ 1.9k
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
3
votes
7
replies
402
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 6 hours ago by ★ 2.3k • written 6 weeks ago by • 0
3
votes
3
replies
127
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 6 hours ago by 141k • written 6 hours ago by • 0
3
votes
9
replies
774
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 5 days ago by ★ 2.4k • written 5 days ago by • 0
3
votes
10
replies
593
views
Piping samtools to R
R NGS bash samtools
6 days ago by joe ▴ 510
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray batch-effect
updated 5 days ago by 43k • written 9.6 years ago by • 0
3
votes
3
replies
152
views
Genbank vs SRA
ncbi genbank genomics sra
updated 1 day ago by ★ 27k • written 1 day ago by ▴ 520
3
votes
4
replies
413
views
biomaRt error for different R version
biomaRt R
updated 5 days ago by 141k • written 6 days ago by ▴ 490
3
votes
4
replies
628
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
1 day ago by rahu • 0
3
votes
3
replies
190
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide Genomic Sequence Uniprot Proteins
updated 1 day ago by 141k • written 1 day ago by ▴ 10
3
votes
2
replies
249
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni R Statistics p-value Fisher
1 day ago by kristiewyleung • 0
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 6 days ago by 43k • written 4.6 years ago by • 0
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq batch-effect DESeq2
updated 6 days ago by 43k • written 4.4 years ago by ▴ 10
3
votes
11
replies
5.9k
views
Modifying R pairs() function
plotMEpairs WGCNA R
updated 6 days ago by 43k • written 6.4 years ago by ▴ 30
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray r GEOquery
updated 6 days ago by 43k • written 5.0 years ago by ▴ 30
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat RNA-Seq batch-effect
updated 6 days ago by 43k • written 4.3 years ago by ▴ 360
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
3
votes
6
replies
611
views
Ciriquant not configuring hisat2 indexed files
ciriquant
1 day ago by Atul K. • 0
3
votes
1
reply
593
views
What is the normalization status of metabric data?
metabric normalization microarray cbioportal
updated 6 days ago by ▴ 20 • written 19 months ago by ★ 4.3k
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
5
replies
523
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
1 day ago by n_navy • 0
3
votes
3
replies
705
views
KissDE and batch effect
kissDE kissplice
1 day ago by david.b.rombaut ▴ 10
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 5 days ago by 43k • written 18 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 5 days ago by 43k • written 7.2 years ago by ▴ 20
2
votes
7
replies
5.2k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated 4 days ago by 81k • written 7.1 years ago by ▴ 80
2
votes
1
reply
275
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun metagenomics blastp taxonomy
updated 4 days ago by 141k • written 4 days ago by • 0
2
votes
5
replies
666
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 3 days ago by ▴ 740 • written 4 days ago by ★ 2.4k
2
votes
4
replies
304
views
SnpEff annotates coding duplication as intronic?
snpeff
6 days ago by kirill.zaslavsky • 0
2
votes
7
replies
796
views
Removing duplicates
duplicates ONT minimap2
updated 5 days ago by ▴ 510 • written 6 days ago by • 0
2
votes
2
replies
1.8k
views
Time point microarray data correcting for batch effects
microarray combat batch-effect
updated 5 days ago by 43k • written 6.7 years ago by ▴ 10
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
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
2
votes
5
replies
419
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats hg002 bed homopolymer-regions
6 days ago by Bikram Kumar • 0
2
votes
5
replies
493
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis MEGA
updated 3 days ago by ★ 27k • written 4 days ago by • 0
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
2
votes
1
reply
2.3k
views
TCGA RNAseqV2 data matrix batch effect control and remove
RNA-Seq batch-effect
updated 5 days ago by 43k • written 7.6 years ago by ▴ 10
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 5 days ago by 43k • written 4.8 years ago by ▴ 20
331 results • Page 2 of 7
Recent Votes
Answer: HaplotypeCaller - only SNPs
Comment: Bwa sampe - BGI
Comment: Redirection of Duplicate PMIDs
Answer: Redirection of Duplicate PMIDs
A: Should I Remove All Positions Containing A Gap In A Multiple Alignment Prior To
Should I Remove All Positions Containing A Gap In A Multiple Alignment Prior To Creating A Phylogenetic Tree?
Answer: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
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Answer: HaplotypeCaller - only SNPs by Pierre Lindenbaum 161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
Answer: Gene set enrichment analysis differences between 2020 and 2024 by geneontologyhelp ▴ 360
We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by GenoMax 141k
Let us know when you find out. Would be a useful thing to know what the data looks like.
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
Yes, that is a very good idea. Thanks for the help!
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by GenoMax 141k
Only thing would be to try them out. See if you can detect them in the data you have. You could also simply look for unique representativ…
Comment: How to calculate identity percentage between proteins contained in a FASTA file? by GenoMax 141k
`clustal omega` can calculate distance matrix between two proteins (makes sense if your proteins are of similar size). You could try that: …
Comment: Should I use unpaired reads from trimmomatic by swbarnes2 14k
If the unpaired are _2, files, the _1 must exist somewhere. But the simple answer is probably going to be to just use all the _2 only. Yo…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by GenoMax 141k
> The needless granularity (fake precision) was obvious from the start You are assuming that all data generated is always of great quality…
Answer: Blasting two protein sequences vs two nucleotide sequences by Istvan Albert 100k
There are various versions of blast, that search in translated spaces, see blastx and tblastn https://blast.ncbi.nlm.nih.gov/Blast.cgi …
Answer: Should I use unpaired reads from trimmomatic by Istvan Albert 100k
If you have lots of data, both paired and unpaired, then the best strategy is probably to treat them separately and merge the counts at the…
Comment: Difference between samtools "-f 9" and "-f 11" by Istvan Albert 100k
It is very easy to make nonsensical flags (unfortunately a flaw of the SAM spec itself) ... not to mention the awkward constructs: a primar…
Comment: Heatmap and rna-seq by Istvan Albert 100k
This forum is dedicated to asking their question on bioinformatics. As long as the topic is bioinformatics, all questions are welcome, and …
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by Istvan Albert 100k
I interpret this as an admission by SRA that phred scores are practically useless. The needless granularity (fake precision) was obvious f…
Comment: TCGA2STAT Error: Firehose connection by Ram 43k
If their github repo is alive, raise an issue there.
Comment: TCGA2STAT Error: Firehose connection by Ngrin • 0
Yeah makes sense. I was following their github. Thanks for pointing this out.
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