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1,000 results • Page 2 of 20
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0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq WGCNA removeBatchEffect DESeq2
updated 3 days ago by 43k • written 7.6 years ago by ▴ 70
3
votes
11
replies
5.9k
views
Modifying R pairs() function
plotMEpairs WGCNA R
updated 3 days ago by 43k • written 6.4 years ago by ▴ 30
0
votes
5
replies
5.8k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 5 hours ago by • 0 • written 6.5 years ago by ▴ 30
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 3 days ago by 43k • written 5.7 years ago by ▴ 620
2
votes
7
replies
5.6k
views
8 follow
How to access specifically 30x NA12878 sequencing runs
giab benchmark fastq wgs data-access
updated 17 days ago by ▴ 360 • written 5.1 years ago by • 0
6
votes
12
replies
5.6k
views
6 follow
Getting sample information from GEO
GEO NCBI
updated 24 days ago by • 0 • written 6.9 years ago by ▴ 350
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome next-gen-sequencing cnv software-error
updated 23 days ago by 43k • written 9.9 years ago by ▴ 870
5
votes
5
replies
5.5k
views
beagle 4 exception: Duplicate marker
vcf IBD plink beagle
updated 24 days ago by 43k • written 9.4 years ago by ▴ 10
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing software-error RNA-seq
updated 10 days ago by • 0 • written 4.7 years ago by ▴ 180
3
votes
2
replies
5.2k
views
RNASeq: Differential gene expression and qqplot
limma differential-gene-expression RNA-Seq deseq2
updated 11 days ago by 43k • written 6.2 years ago by ★ 1.6k
2
votes
7
replies
5.2k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated 1 day ago by 81k • written 7.1 years ago by ▴ 80
2
votes
3
replies
5.1k
views
BLAST Ring Image Generator (BRIG) error
error software alignment
updated 17 days ago by 141k • written 7.4 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 1 day ago by 43k • written 3.7 years ago by • 0
2
votes
7
replies
5.1k
views
9 follow
problem with HOMER findMotifsGenome.pl
HOMER ATAC-Seq
updated 9 days ago by • 0 • written 5.5 years ago by ▴ 80
1
vote
7
replies
5.0k
views
How do I plot several sns.clustermap heatmaps in a single figure?
python seaborn
updated 9 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 9 days ago by • 0 • written 7.5 years ago by ▴ 30
5
votes
15
replies
4.9k
views
6 follow
Why are there many reads with green color in IGV of RNA-seq data?
rna-seq IGV mapping
updated 29 days ago by • 0 • written 4.8 years ago by ▴ 160
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray batch-effect
updated 1 day ago by 43k • written 9.6 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 4 days ago by 43k • written 4.9 years ago by 47k
4
votes
14
replies
4.7k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 23 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 3 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 3 days ago by 43k • written 6.6 years ago by ★ 2.6k
7
votes
3
replies
4.5k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA RNA-Seq batch-effect
updated 2 days ago by 43k • written 5.1 years ago by ▴ 100
4
votes
7
replies
4.5k
views
snakemake output directory
snakemake ngs
updated 4 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 2 days ago by 43k • written 5.9 years ago by ▴ 60
2
votes
2
replies
4.4k
views
Variant calling for sanger reads
variant-calling sanger alignment variants
updated 25 days ago by 43k • written 7.7 years ago by ▴ 70
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq batch-effect
updated 3 days ago by 43k • written 7.4 years ago by ▴ 30
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 11 days ago by 43k • written 7.5 years ago by ▴ 80
12
votes
13
replies
4.4k
views
RNA-Seq DGE using PCA components as covariate
differential-gene-expression RNA-Seq glm DESeq2
updated 11 days ago by 43k • written 6.2 years ago by ★ 1.6k
6
votes
6
replies
4.3k
views
10x to cloupe
single-cell-transcriptomics 10x
11 days ago by firestar ★ 1.6k
11
votes
22
replies
4.1k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 11 days ago by 43k • written 5.0 years ago by ▴ 260
5
votes
20
replies
4.1k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression RNA-seq
updated 11 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 1 day ago by 43k • written 8.7 years ago by ▴ 60
10
votes
6
replies
4.1k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 24 days ago by 43k • written 6.2 years ago by 87k
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor limma sva r batch-effect
updated 1 day ago by 43k • written 7.6 years ago by ★ 1.2k
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 1 day ago by 43k • written 4.6 years ago by ▴ 180
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression Salmon
updated 11 days ago by 43k • written 5.5 years ago by ▴ 100
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq deseq2 batch-effect
updated 2 days ago by 43k • written 4.9 years ago by ▴ 330
7
votes
5
replies
4.0k
views
ISCN annotation for SV/CN VCF files
SV
updated 2 days ago by • 0 • written 7 months ago by ▴ 50
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray r GEOquery
updated 3 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 2 days ago by 43k • written 4.7 years ago by ▴ 30
1
vote
10
replies
3.9k
views
Error in CIBERSORTx
RNA-seq CIBERSORT LM22
updated 6 days ago by ▴ 300 • written 18 months ago by • 0
30
votes
12
replies
3.8k
views
Trying to understand the maths behind one Limma function
limma RNA-Seq batch-effect
updated 4 days ago by 43k • written 4.0 years ago by ▴ 330
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 3 days ago by 43k • written 2.8 years ago by ▴ 60
4
votes
2
replies
3.7k
views
DESeq2 design and batch effect
RNA-Seq batch-effect DESeq2 Salmon
updated 1 day ago by 43k • written 6.5 years ago by ▴ 30
2
votes
4
replies
3.7k
views
Tutorial for analysing gpr files of microarray
GPR microarray
updated 29 days ago by ▴ 10 • written 5.5 years ago by ▴ 190
1
vote
3
replies
3.7k
views
MSF Data Analysis
MSF Proteomics Thermo Proteome Discoverer
updated 16 days ago by • 0 • written 4.4 years ago by ▴ 130
5
votes
8
replies
3.6k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 11 days ago by 43k • written 6.5 years ago by ★ 1.6k
2
votes
6
replies
3.6k
views
Algorithm to remove batch effects
single-cell batch-effect RNA-Seq
updated 3 days ago by 43k • written 3.3 years ago by ▴ 80
7
votes
2
replies
3.6k
views
Timeout on getBM() to retrieve snps from locations
biomaRt getBM R
updated 3 days ago by 43k • written 5.2 years ago by ▴ 600
1,000 results • Page 2 of 20
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Answer: MEGA Analysis Issue on High-Performance Computer
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
Answer: Ubuntu storage space is decreasing automatically
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Answer: Cellranger count error: Input FASTQ file ended prematurely
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Comment: MEGA Analysis Issue on High-Performance Computer by 5heikki 11k
16GB of RAM is nothing. My phone has that. My server has 1TB of RAM, and even that isn't always enough
Comment: MEGA Analysis Issue on High-Performance Computer by GenoMax 141k
I don't think MEGA supports GPU's: https://www.megasoftware.net/web_help_11/Part_I_Getting_Started/Installing_MEGA/System_Requirements.htm
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by ATpoint 81k
You can, if you use RStudio via Docker, for example `bioconductor/bioconductor_docker`. I currently manage many different projects with thi…
Comment: bam merging for archaic samples by Matteo Ungaro ▴ 100
@Pierre Lindenbaum I see. So, I can actually manipulate just one single RG tag at the time with `samtools`? Which flag should I use, or sho…
Comment: bam merging for archaic samples by Pierre Lindenbaum 161k
RG tag "L9302" is missing the the BAM header. You should have something like this in the BAM header ``` @RG ID:L9302 SM:L9302 ``` may be…
Answer: Filtering sam or bam file with maximum matching region by Pierre Lindenbaum 161k
> . Is there any way to find through sam or bam file that which chromosomal position are maximum reads aligning to? samtools depth i…
Comment: Calculate Radius of Gyration [python 3] by ndm1096 • 0
Hello Franco. I am very much new with bioinformatics but I have been tasked with studying the radius of gyration of a timeseries of a prote…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by BioinfGuru ★ 1.7k
That makes a lot more sense. Thank you.
Answer: Removing Illumina microarray probes with no expression HumanHT-12v4 by Gordon Smyth ★ 7.0k
Type ``` help("read.idat") ``` and read the example at the bottom of the page, which shows you how to set the `other$Detection` component o…
Comment: Free/open source 23andme-like analysis by swbarnes2 14k
Accurately assessing a few QC metrics is trivially easy. Assessing the significance of variants in a clinically responsible way is really…
Comment: Cellranger count error: Input FASTQ file ended prematurely by swbarnes2 14k
If _1 and _2 really are the same library, you should rename the fastqs, or make symlinks, such that they have the same sample name, but dif…
Comment: Cellranger count error: Input FASTQ file ended prematurely by ATpoint 81k
Just delete the index read files. They just take up space and will never be used.
Comment: Adding CB tag to bam file by swbarnes2 14k
Yes. Why wouldn't you use, say, AddOrReplaceReadsGroups?
Comment: Ciriquant not configuring hisat2 indexed files by Atul K. • 0
Thank you. Decreased the threads to 2 (changed the threads: 2 in the config file; but it was somehow using 4). It did run for sometime but …
Answer: GTF file from Stringtie to R Studio for either Ballgown or DESeq2 by Ram 43k
See this section on how to use tximport to import StringTie output for DESeq2 processing: https://bioconductor.org/packages/devel/bioc/vign…
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