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934 results • Page 1 of 19
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76
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72
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20k
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19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
15 days ago by Kevin Blighe 87k
10
votes
37
replies
13k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato gene
updated 29 days ago by • 0 • written 8.8 years ago by ▴ 170
10
votes
36
replies
5.9k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA batch-effect DESeq2 R
updated 23 days ago by 43k • written 5.7 years ago by ▴ 620
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 7 days ago by • 0 • written 12.8 years ago by ★ 1.7k
87
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 22 days ago by • 0 • written 3.6 years ago by 3.2k
38
votes
24
replies
2.0k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 9 days ago by 19k • written 12 days ago by ▴ 580
23
votes
23
replies
9.9k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq removeBatchEffect batch-effect edger
updated 22 days ago by 43k • written 5.3 years ago by ▴ 130
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 23 days ago by 43k • written 6.8 years ago by ★ 1.3k
7
votes
20
replies
6.5k
views
7 follow
Repeat masked gtf files from ensembl
ensembl RNA-Seq genome
updated 28 days ago by ▴ 210 • written 4.3 years ago by ▴ 80
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 21 days ago by 43k • written 4.6 years ago by ★ 1.4k
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter visualization R
updated 23 days ago by 43k • written 9.6 years ago by ▴ 100
8
votes
16
replies
1.1k
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 13 days ago by ★ 2.4k • written 9 weeks ago by • 0
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 2 days ago by 161k • written 5.7 years ago by ▴ 180
7
votes
16
replies
778
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
11 days ago by Ruqaiya • 0
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read length bam
updated 20 days ago by ▴ 10 • written 10.2 years ago by ▴ 180
0
votes
16
replies
1.1k
views
What is the sequence origin in human plasma?
human sequence cfDNA
26 days ago by biwdpang • 0
4
votes
15
replies
1.6k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR DESeq Differential-Expression RNA-Seq
updated 6 days ago by ★ 7.1k • written 4 months ago by ▴ 10
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt trimming crispr sequencing
updated 7 days ago by 142k • written 4.5 years ago by ▴ 20
5
votes
14
replies
1.1k
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications dorado basecalling nanopore methylation
updated 28 days ago by 142k • written 7 weeks ago by ▴ 20
13
votes
14
replies
806
views
High Malat-1 expression in single cell data
single-cell
updated 2 days ago by ▴ 40 • written 10 days ago by ▴ 40
10
votes
14
replies
658
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 2 days ago by 142k • written 8 days ago by • 0
5
votes
13
replies
1.7k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 19 days ago by 82k • written 20 days ago by ★ 1.7k
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun silva blast
updated 15 days ago by • 0 • written 2.2 years ago by ▴ 10
4
votes
13
replies
971
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 23 days ago by ★ 1.7k • written 28 days ago by • 0
5
votes
13
replies
9.3k
views
8 follow
biomaRt: Timeout on getBM().
r biomart ensembl
updated 28 days ago by ★ 2.0k • written 2.8 years ago by ▴ 40
4
votes
12
replies
4.8k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 17 hours ago by ▴ 180 • written 3.0 years ago by ▴ 20
16
votes
12
replies
7.4k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome perl python3 bash python
updated 6 days ago by ▴ 10 • written 3.1 years ago by ▴ 120
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 21 days ago by • 0 • written 12.1 years ago by ★ 2.9k
11
votes
12
replies
1.1k
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated 21 days ago by 43k • written 21 days ago by • 0
30
votes
12
replies
3.9k
views
Trying to understand the maths behind one Limma function
limma RNA-Seq batch-effect
updated 24 days ago by 43k • written 4.0 years ago by ▴ 330
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq deseq2 batch-effect
updated 22 days ago by 43k • written 5.0 years ago by ▴ 330
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression TPM RNA-Seq counts batch-effect
22 days ago by Ram 43k
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA gene-expression R
updated 23 days ago by 43k • written 5.3 years ago by ▴ 120
25
votes
11
replies
3.8k
views
6 follow
Forum: Site Use Guidelines
meta biostars Guidelines
updated 16 days ago by 43k • written 14.6 years ago by 100k
2
votes
11
replies
2.6k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 1 day ago by • 0 • written 4.8 years ago by ▴ 60
2
votes
11
replies
953
views
Questions about a bug when transferring cram file to bam file
sequence samtools bcftools
updated 10 days ago by ★ 1.2k • written 22 days ago by • 0
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 13 days ago by ★ 3.8k • written 10.8 years ago by ▴ 920
1
vote
11
replies
5.5k
views
Truncated Bam Error
R next-gen sequencing software error
updated 4 days ago by • 0 • written 6.1 years ago by ▴ 20
3
votes
11
replies
6.0k
views
Modifying R pairs() function
plotMEpairs WGCNA R
updated 23 days ago by 43k • written 6.5 years ago by ▴ 30
4
votes
11
replies
843
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 16 days ago by 4.2k • written 17 days ago by • 0
23
votes
11
replies
4.9k
views
7 follow
Code golf: detecting homopolymers of length N in the (human) genome
code golf fasta homopolymer repeat
updated 23 days ago by 43k • written 5.0 years ago by 47k
0
votes
11
replies
669
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
14 days ago by atowns21 • 0
8
votes
10
replies
787
views
bash script
whole-genome-sequencing
updated 24 days ago by 43k • written 4 weeks ago by ▴ 30
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 10 days ago by ▴ 40 • written 6.8 years ago by ★ 1.3k
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq batch-effect
updated 23 days ago by 43k • written 7.4 years ago by ▴ 30
9
votes
10
replies
7.0k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat scRNA-seq Harmony RNA-seq batch-effect
updated 21 days ago by 43k • written 4.6 years ago by ▴ 140
1
vote
10
replies
858
views
error to run rnammer
phylogenomics rRNA_extraction rnammer
updated 4 days ago by • 0 • written 4 months ago by ▴ 30
0
votes
10
replies
571
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 9 days ago by 19k • written 17 days ago by • 0
7
votes
10
replies
2.7k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch batch-effect DESeq2 rna-seq
updated 23 days ago by 43k • written 2.1 years ago by ▴ 60
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 23 days ago by 43k • written 7.4 years ago by • 0
934 results • Page 1 of 19
Recent Votes
Comment: Importing a fastq file
EdgeR - relationship between logFC and coefficients
Answer: EdgeR - relationship between logFC and coefficients
Detecting highly variable genes within replicates
Detecting highly variable genes within replicates
A: Detecting highly variable genes within replicates
How to set a threshold for coefficient of variation in RNA-seq?
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Popular Question to Amr ▴ 160
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Recent Replies
Comment: LncRNA Nomenclature by jain72744 ▴ 10
My data is based on gene counts and the respective gene IDs are given so I should work with ENSGs? lncRNA_transcripts <- getBM(attributes …
Answer: DESeq2 error by ATpoint 82k
At least one group needs replication. That is the short answer. For a longer answer add details on experimental design.
Comment: When should I use R-MarkDown over R-Script ? by ATpoint 82k
What is your motivation to ask? Add some context. Beyond that, always use Rmd unless you write package code.
Comment: LncRNA Nomenclature by ATpoint 82k
RNA-seq is typically analyzed on gene rather than transcript level. Are your counts gene or transcript?
Comment: EdgeR - relationship between logFC and coefficients by gBioStar5 ▴ 10
Thanks a lot, this was very helpful. I'll keep that in mind.
Answer: EdgeR - relationship between logFC and coefficients by Gordon Smyth ★ 7.1k
Results presented by topTags() are on the log2 scale. Coefficients stored internally in the DGELRT object are on the loge scale. If you con…
Answer: Importing a fastq file by size_t ▴ 120
run command `explorer.exe .` in wsl terminal, and then drag file to folder
Comment: Contig assembly task, errors by Philipp Bayer 8.4k
Hi Ricardo! CAP3 is an 'older' overlap assembler from 1999 which is perfectly suited for these kinds of 'small' tasks. I used it last in my…
Comment: absolute path for symbolic links in Snakefile by Jesse ▴ 770
That's really handy, and much more of a general solution than stripping off the directory names! So yifangt86, if you're on Linux you can …
Comment: Truncated metadata file report from ENA Portal API by GenoMax 142k
Are you missing a `"` at the end of the URL. Doing wget -O test.out "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=PRJNA43…
Comment: Different output for read length by marco.barr ▴ 100
very strange, I double checked the BAM file and it is the same one I used for your request. Are the commands I wrote above correct? How is …
Comment: Different output for read length by Pierre Lindenbaum 161k
the first read as a length of 1747, i wonder how you can just find '50' $ wget -qO - "https://gist.githubusercontent.com/Macdot3/4650…
Comment: Problem with Seurat package in PercentageFeatureSet function by bk11 ★ 2.4k
Yes, `CreateAssayObject` function is used for only expression matrix.
Comment: Different output for read length by marco.barr ▴ 100
Here is my result, I hope you can see it. [https://gist.github.com/Macdot3/4650243a10540d8c06f728ffc16a136c][1] [1]: https://gist.gith…
Comment: Different output for read length by marco.barr ▴ 100
I just published my link on paste, why can't I see my public paste on the site?
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