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182
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different protocols for rapid nanopore sequencing starting from solid tumor
solid tumor nanopore oxford sequencing
updated 9 weeks ago by 142k • written 9 weeks ago by 4.2k
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0
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178
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Questions regarding Boundary Conditions for Adaptive Sequencing for Oxford Nanopore
adaptive sampling nanopore oxford sequencing
9 weeks ago by LauferVA 4.2k
2
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7
replies
740
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Selecting query format for repeated calls to NCBI's API
NCBI esummary elink API efetch
updated 7 weeks ago by 142k • written 12 weeks ago by 4.2k
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5
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435
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Linking metadata in non-Pubmed Commons indexed journal articles to records housed by NCBI
NCBI Entrez SRA Journal Metadata
12 weeks ago by LauferVA 4.2k
2
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8
replies
1.0k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature HGVS
updated 11 weeks ago by ▴ 560 • written 5 months ago by 4.2k
0
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1
reply
366
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Software for Spatial Transcriptomic data [NanoString; Visium]?
NanoString Visium Spatial-Transcriptomics 10X
5 months ago by LauferVA 4.2k
1
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4
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617
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Indexing pubmed articles by data available?
search data pubmed query
6 months ago by LauferVA 4.2k
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0
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356
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Current landscape of approaches to scRNA-seq with nanopore sequencers?
scRNA-seq nanopore single-cell
7 months ago by LauferVA 4.2k
3
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2
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521
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Scanning for ultra-hot topics in science via pubmed, or using other tools
growth pubmed
7 months ago by LauferVA 4.2k
3
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4
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620
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Whole transcriptome analysis nominated primarily miRNA-related pathways. Advice?
miRNA RNA-seq QC GSEA
9 months ago by LauferVA 4.2k
1
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6
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839
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cBioPortal data with negative log2(FPKM + 1) values
FPKM cBioPortal
10 months ago by LauferVA 4.2k
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0
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308
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Is anyone aware of a function that will create a MultiAssayExperiment() based on the structure of flat files?
processing File MultiAssayExperiment Automation
10 months ago by LauferVA 4.2k
5
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2
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832
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Tools for sentiment analysis that have been vetted on pubmed abstracts
sentiment-analysis pubmed Python R
updated 11 months ago by 43k • written 11 months ago by 4.2k
8
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9
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1.8k
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6 follow
Advantages of install.packages() versus BiocManager::install()
R bioconductor
10 months ago by LauferVA 4.2k
2
votes
1
reply
505
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Choosing the right batch effect control algorithm for bulk RNA-seq data meta-analysis
PEER SVA RUV RNA-seq
updated 11 months ago by ★ 2.9k • written 11 months ago by 4.2k
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0
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512
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What are the existing proposals for how to approach genomic coordinates in a pangenome reference environment?
coordinates pangenome genomic
11 months ago by LauferVA 4.2k
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0
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473
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Different alternatives for downloading GWAS summary statistics en masse
GWAS
11 months ago by LauferVA 4.2k
1
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0
replies
353
views
List of Ongoing and Planned Long Read Sequencing studies?
long-read-sequencing third-generation
updated 13 months ago by 43k • written 13 months ago by 4.2k
1
vote
2
replies
609
views
Clinical Informatics Tool like DAVID
informatics UMLS annotation clinical SNOMED
updated 16 months ago by 142k • written 16 months ago by 4.2k
0
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0
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304
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Clinical Informatics - Labelling ICD-10 codes with desired annotations
i3b3 SNOMED UMLS
16 months ago by LauferVA 4.2k
1
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7
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1.7k
views
Tool to download all PDFs associated with results to a pubmed query?
eUtils NCBI pubmed entrez
updated 16 months ago by ▴ 290 • written 18 months ago by 4.2k
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0
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512
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Best options for tools going from (complex) substitution name to sequence and/or from sequence to complex substitution name
cDNA SNV Sequence HGVS Fasta
20 months ago by LauferVA 4.2k
2
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2
replies
603
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Simplest solution to generate nucleotide sequence with and without a variant (all in one)
context nucleotide
20 months ago by LauferVA 4.2k
4
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3
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914
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Mapping GeneSymbol plus cDNA position to a Chr:Position ... without transcript ID.
annotation splice site transcript build
21 months ago by LauferVA 4.2k
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0
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364
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Drilling down to the right samples in COSMIC
cosmic mutational PCAWG SBS tumor signature
21 months ago by LauferVA 4.2k
1
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0
replies
327
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Finding Specific Types of Data for Cancer Studies
TCGA GDC Cancer Entrez GEO
21 months ago by LauferVA 4.2k
3
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9
replies
1.6k
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Extract nucleotide sequence from a RefSeq Transcript ID
nucleotide refseq transcript sequence entrez
21 months ago by LauferVA 4.2k
4
votes
3
replies
1.5k
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Tips and tricks for using ImageJ
imageJ macros automation
updated 22 months ago by ▴ 910 • written 22 months ago by 4.2k
0
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0
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397
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Different types of repeat elements in eukaryotic genomes
repeat sequence genome graph STR satellite
2.2 years ago by LauferVA 4.2k
5
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6
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1.2k
views
Existing tutorials using Docker to set up and run any type of NGS workflow?
docker NGS pipeline automate workflow
2.2 years ago by LauferVA 4.2k
0
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0
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473
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Running / Debugging Encode-DCC RNA-seq pipeline
RNA-seq Encode
2.4 years ago by LauferVA 4.2k
4
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5
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1.3k
views
6 follow
Is there a database of bioinformatics tools & databases?
ebi entrez
updated 15 months ago by 43k • written 2.4 years ago by 4.2k
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2
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1.9k
views
In a locuszoom file, what does a column title "pp" contain?
fineMap locuszoom pp
updated 2.1 years ago by 43k • written 9.3 years ago by 4.2k
1
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2
replies
1.3k
views
Where to learn about getting a few thousand genomes sequenced?
budget sequencing
updated 15 months ago by 43k • written 9.0 years ago by 4.2k
0
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1
reply
777
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Is there a database or catalog of the proteins secreted through the Type 3 Secretion System available?
Microbiology Metagenomics
3.8 years ago by LauferVA 4.2k
0
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0
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808
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Programmatically kicking off cellranger based on fastq folder format
10x fastq cellranger scRNA-seq
3.9 years ago by LauferVA 4.2k
0
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7
replies
3.9k
views
Locus Zoom Issuing "No valid markers in VCF file" on a VCF created in Plink 1.9
plink2 VCF LocusZoom
updated 4.9 years ago by • 0 • written 8.0 years ago by 4.2k
1
vote
1
reply
1.1k
views
Go Partition Database or another like tool
gene ontology hierarchy GO DAG
4.9 years ago by LauferVA 4.2k
2
votes
0
replies
969
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Options for labeling pathways with higher-order ontologies
pathways gene ontology KEGG Biocarta GO
4.9 years ago by LauferVA 4.2k
15
votes
4
replies
9.1k
views
Selection of a "suggestive" level of association in a GWAS study
association GWAS statistics
11 months ago by LauferVA 4.2k
5
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2
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2.6k
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How to print locuszoom plot at 300 dpi or greater
locuszoom publication resolution figures
updated 5.7 years ago by 43k • written 8.2 years ago by 4.2k
3
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8
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1.4k
views
Function returning % trait explained for a SNP given effect size, MAF, prevalence, etc. for a complex trait
risk score genetic variance explained R
updated 5.8 years ago by 11k • written 5.8 years ago by 4.2k
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2
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1.8k
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High-quality visualization of GSEA data illustrating relationships between multiple pathways.
GSEA figure
6.2 years ago by LauferVA 4.2k
10
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6
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5.0k
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Varying Sample Size vs Read Depth, Read Length, and Single vs Paired end to optimize DE analysis of RNA-Seq
RNA-Seq read-depth mapping
updated 21 months ago by 43k • written 8.4 years ago by 4.2k
1
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3
replies
1.8k
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Conditioning association summary statistics using a correlation matrix.
conditional analysis imputation fine-mapping
6.4 years ago by LauferVA 4.2k
1
vote
2
replies
1.4k
views
Are WGS cohorts with large numbers of global participants (larger than 1kg) publicly available?
WGS 1000 genomes 1kg
6.5 years ago by LauferVA 4.2k
4
votes
4
replies
3.2k
views
Best implementation of negative binomial association test for GWAS data?
statistics negative binomial GWAS association
updated 2.1 years ago by 43k • written 9.3 years ago by 4.2k
3
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1
reply
4.0k
views
What makes assigning A/T and G/C SNPs to a strand unreliable if MAF is not near 0.5?
A/T G/C SNP Strand
6.8 years ago by LauferVA 4.2k
5
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3
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2.4k
views
Methods of classifying, not detecting, structural variation?
SV-annotation-algorithm Structural-variation
updated 21 months ago by 43k • written 8.4 years ago by 4.2k
0
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0
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1.3k
views
Do imputed variants tend to show weaker, stronger, or the same average association compared to genotyped variants
imputation genotyped SNP GWAS
6.9 years ago by LauferVA 4.2k
86 results • Page 1 of 2
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