Limit : this month
all time today this week this month this year
1,000 results • Page 5 of 20
Sort: Votes
Rank Views Votes Replies
3
votes
5
replies
413
views
Losing my mind with a VCF problem
vcf bcftools
updated 27 days ago by 54k • written 28 days ago by ▴ 50
3
votes
2
replies
1.1k
views
Issues Using DMRcate and rmSNPandCH
DMRcate R
updated 16 days ago by ▴ 20 • written 14 months ago by ▴ 10
3
votes
5
replies
643
views
somatic variant calling without matched normal in long-reads
variants cancer illumina ONT nanopore
24 days ago by eesiribloom ▴ 80
3
votes
0
replies
173
views
Herald: The Biostar Herald for Monday, March 25, 2024
herald
25 days ago by Biostar 2.6k
3
votes
1
reply
6.1k
views
Normalization before or after merging the samples in Seurat
single-cell seurat batch-effect
updated 2 days ago by 43k • written 3.3 years ago by ▴ 80
3
votes
1
reply
154
views
NCBI CLI Download all proteins from Taxid
ncbi
updated 17 days ago by 141k • written 17 days ago by ★ 1.9k
3
votes
4
replies
351
views
How to download large-scale cDNA sequences from NCBI effectively ?
NCBI. cDNA
updated 6 days ago by 161k • written 6 days ago by ▴ 10
3
votes
7
replies
570
views
Blast NCBI online using R
R NCBI BLAST Rstudio
24 days ago by Begonia_pavonina ▴ 150
3
votes
12
replies
475
views
struggle to get fasta files from ucsc goldenPath
ucsc getfasta fasta
17 days ago by Lila M ★ 1.2k
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor batch-effect
updated 23 hours ago by 43k • written 7.9 years ago by ★ 3.4k
3
votes
2
replies
326
views
FDR and Bonferroni
FDR Bonferroni
updated 22 days ago by ▴ 510 • written 24 days ago by • 0
3
votes
10
replies
575
views
Piping samtools to R
R NGS bash samtools
2 days ago by joe ▴ 510
3
votes
1
reply
443
views
Can anyone give me the code for in-silico digestion of whole genome with two restriction enzyme in "R" through Biostrings package?
whole-genome In-silico-digestion
updated 11 days ago by 43k • written 13 days ago by ▴ 10
3
votes
3
replies
612
views
Why are there several gene expression files (for example, miRNA) in TCGA for one case?
Differential-gene-expression TCGA miRNA
updated 10 days ago by 43k • written 5 months ago by ▴ 260
3
votes
5
replies
396
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
updated 16 days ago by 141k • written 17 days ago by ▴ 200
3
votes
2
replies
217
views
Interproscan taking so much time
slurm interproscan transcriptomics
updated 22 days ago by ★ 1.9k • written 22 days ago by ▴ 10
3
votes
1
reply
255
views
how to change the gene header names in a fasta file?
fasta bioawk awk seqkit
updated 7 days ago by 43k • written 7 days ago by • 0
3
votes
5
replies
1.4k
views
Removing Batch effect that is the same as condition - DESEq2
RNA-Seq batch-effect DESeq2
updated 11 days ago by 43k • written 3.9 years ago by • 0
3
votes
5
replies
1.8k
views
Limma/edgeR Design matrix for gender effect
RNA-Seq batch-effect
updated 2 days ago by 43k • written 4.7 years ago by • 0
3
votes
7
replies
951
views
How much adapters is it ok to keep in my samples after RNA seq?
RNA-seq illumina adapters
updated 14 days ago by 43k • written 5 months ago by ▴ 150
3
votes
5
replies
665
views
How to filter Illumina Nirvana variant annotation?
nirvana filtration
updated 26 days ago by 161k • written 26 days ago by • 0
3
votes
10
replies
8.4k
views
6 follow
GATK HaolotypeCaller takes too much time for variant calling
HaplotypeCaller GATK
updated 14 days ago by 43k • written 6.4 years ago by ▴ 910
3
votes
2
replies
294
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics Single-Cell
updated 14 days ago by 43k • written 7 weeks ago by ▴ 20
3
votes
4
replies
363
views
biomaRt error for different R version
biomaRt R
updated 1 day ago by 141k • written 2 days ago by ▴ 490
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 1 day ago by 43k • written 7.1 years ago by ▴ 310
3
votes
5
replies
443
views
Having trouble building VG in Ubuntu
vg
updated 5 days ago by 43k • written 8 days ago by • 0
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray r GEOquery
updated 2 days ago by 43k • written 5.0 years ago by ▴ 30
3
votes
2
replies
2.1k
views
Batch effect correction - miRNA sequencing - DESeq2
Batch-effect DESeq2 miRNA-Seq
updated 2 days ago by 43k • written 5.4 years ago by • 0
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat RNA-Seq batch-effect
updated 2 days ago by 43k • written 4.3 years ago by ▴ 360
3
votes
3
replies
310
views
How do I find up-to-date gene symbols for outdated names
names symbols gene
12 days ago by DSmith • 0
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq combat rna-seq sva batch-effect
updated 2 days ago by 43k • written 21 months ago by ▴ 20
3
votes
7
replies
506
views
Artificial deletion in bam
bam
updated 14 days ago by ★ 1.2k • written 15 days ago by ▴ 10
3
votes
3
replies
512
views
How to run BRIG on Ubuntu 22?
BRIG Ubuntu
updated 16 days ago by • 0 • written 3 months ago by ▴ 710
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 23 hours ago by 43k • written 4.6 years ago by ▴ 180
3
votes
6
replies
879
views
Any problem re-using last year's RNA-Seq data in this year's analysis?
RNA-Seq batch-effect
updated 2 days ago by 43k • written 3.7 years ago by ▴ 20
3
votes
4
replies
335
views
Single cell analysis with "meta".tsv.gz file
Single-cell
16 days ago by Estevão • 0
3
votes
3
replies
206
views
TMM normalization with DESeq2
RNA-seq DESeq2
updated 17 days ago by 43k • written 17 days ago by ▴ 60
3
votes
3
replies
761
views
GATK error on HPC clusters
variant-calling SNP
updated 17 days ago by 43k • written 12 months ago by • 0
3
votes
1
reply
580
views
What is the normalization status of metabric data?
metabric normalization microarray cbioportal
updated 1 day ago by ▴ 20 • written 19 months ago by ★ 4.3k
3
votes
5
replies
1.3k
views
NextGen Sequencing Folks, what do you keep as your raw backup? BCL's or FASTQ's? Both?
next-gen-sequencing backups data-storage
updated 14 days ago by 43k • written 2.1 years ago by ▴ 130
3
votes
4
replies
360
views
Genome completeness and contamination: CheckM vs CheckM2
genome-completeness contamination
14 days ago by beacamara • 0
3
votes
5
replies
1.3k
views
How to identify antibiotic resistant genes in gene databases?
antibiotic Gene-Ontology GO
updated 8 days ago by 43k • written 2.0 years ago by • 0
3
votes
3
replies
312
views
Visualize pathways from MSigDB
MSigdb
13 days ago by Chris ▴ 260
3
votes
1
reply
2.1k
views
Maximum Number of Gene in a DESeq2 and edgeR
Differential-Gene-Expression EdgeR DESeq2
updated 10 days ago by 43k • written 8.1 years ago by ▴ 10
3
votes
12
replies
719
views
Facing problem with extracting phenotypic data from GEO
WGCNA GEO
23 days ago by bioinfo_enthusiast • 0
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq batch-effect DESeq2
updated 2 days ago by 43k • written 4.4 years ago by ▴ 10
3
votes
2
replies
803
views
Retrieve initial query in getBM()
getBM biomaRt R gene
updated 2 days ago by 43k • written 3.1 years ago by • 0
3
votes
2
replies
539
views
News: Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of the 'Other' Endocrine Regulatory Systems in Health and Disease", Vol…
mathematical-modelling endocrinology ML systems-biology machine-learning
21 days ago by Johannes W. Dietrich • 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 2 days ago by 43k • written 2.8 years ago by ▴ 60
3
votes
6
replies
10k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker Masking
updated 3 days ago by ▴ 10 • written 7.5 years ago by ▴ 10
1,000 results • Page 5 of 20
Recent Votes
Answer: Duplicate marking, read names, and the SRA
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Answer: Cellranger count error: Input FASTQ file ended prematurely
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
Recent Locations • All
india, just now
United States, 1 minute ago
USA, 1 minute ago
United States, 2 minutes ago
Spain, 4 minutes ago
Oviedo, 5 minutes ago
United Kingdom, 6 minutes ago
Recent Awards • All
Popular Question to Rodolfo Adrián • 0
Scholar to damian.szk ▴ 70
Popular Question to alphaflylizard • 0
Scholar to GenoMax 141k
Popular Question to Shicheng Guo ★ 9.4k
Popular Question to DanielEB_fisk ▴ 20
Scholar to Pierre Lindenbaum 161k
Recent Replies
Comment: Duplicate marking, read names, and the SRA by Luka • 0
>In many cases those remain recoverable using the -F option when you dump the data (cloud download not required) The -F option (or any equ…
Answer: Duplicate marking, read names, and the SRA by GenoMax 141k
To be specific, not every dataset in SRA loses the original identifiers. In many cases those remain recoverable using the `-F` option when …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by Ram 43k
To use different versions of R and bioconductor, you don't really need RStudio. One can simply create new conda environments with the requi…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by BioinfGuru ★ 1.7k
Done. Thank you.
Comment: Installing/switching between versions of R/Rstudio/Bioconductor by GenoMax 141k
Perhaps add the word linux/ubuntu to the title? You have noted that the instructions are for Ubuntu in text.
Comment: Installing/switching between versions of R/Rstudio/Bioconductor by BioinfGuru ★ 1.7k
Thanks @Ram I'll add that to the intro. I'm the admin on my machine so I haven't found it necessary to install any other way. I'll try a fr…
Comment: Downloading the raw microarray data from GEO by GenoMax 141k
No GPR files with this data unless you ask the submitters for them directly. You can find the matrix of data here: https://ftp.ncbi.nlm.nih…
Comment: Cellranger count error: Input FASTQ file ended prematurely by GenoMax 141k
That is odd. Thanks for following-up and providing an explanation.
Answer: Cellranger count error: Input FASTQ file ended prematurely by bp22 ▴ 70
Dear all, The reason for the error was due to the index (I1) fastq files, for example `SI-GA-A1_1_S1_L001_I1_001.fastq.gz` having a lo…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor by Ram 43k
Your tutorial required `sudo` and thus is not doable for a majority of people. Any alternative to `sudo snap`?
Comment: Should I apply doublet detection for each pool seperately? by Ram 43k
Do not delete posts that have received feedback,
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues by _quantum_girl_ ▴ 10
They aren't merging any datasets. Just for reference the paper is this: https://www.nature.com/articles/s41380-022-01674-9#MOESM1. Citing: …
Comment: RNA seq differential expression analysis by BioinfGuru ★ 1.7k
https://help.galaxyproject.org/
Answer: RNA seq differential expression analysis by Mohamed Abderrahmane ▴ 10
The tool RSEM, which performs transcript quantification for RNA-Seq data, provides FPKM.
Comment: Illumina reads preprocessing best practice for snp calling applications by Enrique • 0
Hi! I'm still interested in the step that you use for the SNP calling. Did you use `trimmomatic` or another tool for trimming before mappin…
Traffic: 2552 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6