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1,131 results • Page 2 of 23
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3
votes
11
replies
5.9k
views
Modifying R pairs() function
plotMEpairs WGCNA R
updated 8 days ago by 43k • written 6.4 years ago by ▴ 30
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 5 days ago by • 0 • written 6.5 years ago by ▴ 30
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 7 hours ago by ▴ 850 • written 6.1 years ago by ▴ 10
10
votes
36
replies
5.8k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA batch-effect DESeq2 R
updated 8 days ago by 43k • written 5.7 years ago by ▴ 620
2
votes
7
replies
5.7k
views
8 follow
How to access specifically 30x NA12878 sequencing runs
giab benchmark fastq wgs data-access
updated 23 days ago by ▴ 360 • written 5.1 years ago by • 0
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome next-gen-sequencing cnv software-error
updated 28 days ago by 43k • written 9.9 years ago by ▴ 870
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing software-error RNA-seq
updated 15 days ago by • 0 • written 4.7 years ago by ▴ 180
2
votes
7
replies
5.2k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated 6 days ago by 82k • written 7.2 years ago by ▴ 80
3
votes
2
replies
5.2k
views
RNASeq: Differential gene expression and qqplot
limma differential-gene-expression RNA-Seq deseq2
updated 16 days ago by 43k • written 6.2 years ago by ★ 1.6k
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 7 days ago by 43k • written 3.7 years ago by • 0
2
votes
3
replies
5.1k
views
BLAST Ring Image Generator (BRIG) error
error software alignment
updated 22 days ago by 141k • written 7.4 years ago by ▴ 20
2
votes
7
replies
5.1k
views
9 follow
problem with HOMER findMotifsGenome.pl
HOMER ATAC-Seq
updated 14 days ago by • 0 • written 5.5 years ago by ▴ 80
8
votes
5
replies
5.1k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by ▴ 60
1
vote
7
replies
5.1k
views
How do I plot several sns.clustermap heatmaps in a single figure?
python seaborn
updated 15 days ago by ▴ 40 • written 3.4 years ago by ▴ 880
0
votes
1
reply
5.0k
views
How to compute a one tail (one way) log rank test for survival?
R survival hypothesis-testing log-rank
updated 14 days ago by • 0 • written 7.5 years ago by ▴ 30
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray batch-effect
updated 7 days ago by 43k • written 9.7 years ago by • 0
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 9 days ago by 43k • written 5.0 years ago by 47k
4
votes
14
replies
4.8k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 29 days ago by 43k • written 22 months ago by ▴ 20
1
vote
9
replies
4.7k
views
Help with multiple batch effects
sva combat batch-effect
updated 8 days ago by 43k • written 5.8 years ago by ▴ 30
1
vote
2
replies
4.6k
views
predict TF binding sites from DNA sequence
TF TRANSFAC TFBS binding-site
updated 9 days ago by 43k • written 6.6 years ago by ★ 2.6k
7
votes
3
replies
4.6k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA RNA-Seq batch-effect
updated 8 days ago by 43k • written 5.1 years ago by ▴ 100
4
votes
7
replies
4.5k
views
snakemake output directory
snakemake ngs
updated 9 days ago by • 0 • written 3.9 years ago by ▴ 200
2
votes
4
replies
4.5k
views
Differential Expression Analysis with monocle and batch effect correction
single-cell RNA-Seq batch-effect
updated 8 days ago by 43k • written 5.9 years ago by ▴ 60
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq batch-effect
updated 8 days ago by 43k • written 7.4 years ago by ▴ 30
12
votes
13
replies
4.4k
views
RNA-Seq DGE using PCA components as covariate
differential-gene-expression RNA-Seq glm DESeq2
updated 16 days ago by 43k • written 6.2 years ago by ★ 1.6k
18
votes
20
replies
4.4k
views
6 follow
How to identify significant differentially expressed genes and gene regulatory networks from microarray data.
microarray differential-gene-expression
updated 16 days ago by 43k • written 7.5 years ago by ▴ 80
6
votes
6
replies
4.3k
views
10x to cloupe
single-cell-transcriptomics 10x
16 days ago by firestar ★ 1.6k
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 16 days ago by 43k • written 5.0 years ago by ▴ 260
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression RNA-seq
updated 16 days ago by 43k • written 6.2 years ago by ▴ 90
3
votes
2
replies
4.1k
views
Batch effects in sequencing data
batch-effect
updated 7 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 7 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 7 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 8 days ago by 43k • written 4.9 years ago by ▴ 330
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression Salmon
updated 16 days ago by 43k • written 5.5 years ago by ▴ 100
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray r GEOquery
updated 8 days ago by 43k • written 5.0 years ago by ▴ 30
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq batch-effect
updated 8 days ago by 43k • written 4.8 years ago by ▴ 30
1
vote
10
replies
3.9k
views
Error in CIBERSORTx
RNA-seq CIBERSORT LM22
updated 11 days ago by ▴ 300 • written 18 months ago by • 0
3
votes
4
replies
3.8k
views
Error in ComBat function: Error in dat[, batch == batch_level] : (subscript) logical subscript too long
Batch-effect microarray R
updated 8 days ago by 43k • written 2.8 years ago by ▴ 60
30
votes
12
replies
3.8k
views
Trying to understand the maths behind one Limma function
limma RNA-Seq batch-effect
updated 10 days ago by 43k • written 4.0 years ago by ▴ 330
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq batch-effect DESeq2 Salmon
updated 7 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 2 days ago by 43k • written 14.6 years ago by 100k
1
vote
3
replies
3.7k
views
MSF Data Analysis
MSF Proteomics Thermo Proteome Discoverer
updated 21 days ago by • 0 • written 4.4 years ago by ▴ 130
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 16 days ago by 43k • written 6.5 years ago by ★ 1.6k
2
votes
6
replies
3.7k
views
Algorithm to remove batch effects
single-cell batch-effect RNA-Seq
updated 8 days ago by 43k • written 3.3 years ago by ▴ 80
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt getBM R
updated 8 days ago by 43k • written 5.2 years ago by ▴ 600
2
votes
6
replies
3.6k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell RNAseq DE Analysis Treatment Control
updated 4 hours ago by 82k • written 3.9 years ago by ▴ 280
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 7 days ago by 43k • written 4.5 years ago by ▴ 140
8
votes
12
replies
3.5k
views
Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, respectively
ATAC-seq
updated 22 days ago by • 0 • written 3.4 years ago by ▴ 40
0
votes
13
replies
3.5k
views
6 follow
Tax4Fun2 - error
tax4fun silva blast
updated 1 day ago by • 0 • written 2.2 years ago by ▴ 10
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 7 days ago by 43k • written 7.1 years ago by ▴ 310
1,131 results • Page 2 of 23
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So I used the barcodes that I created (combos of positions 1-10 and 11-20) and I obtained similar alignment stats as the paper I pulled the…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
Thank you so much, it actually worked!
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Hi @efc1e545 , First a caveat. the information we most need in order to help guide you to a successful conclusion is not provided in thi…
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The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unle…
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Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
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Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
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Open a new question, with details.
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I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
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thank you!
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Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
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> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
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This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
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I think when you give indent to seuObj : ```r Idents(seuObj) <- 'RNA_snn_res.0.1' ``` You may wrongly assign other value to it such as `…
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In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
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In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
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