Entering edit mode
4 weeks ago
Shicheng Guo
★
9.4k
I'm seeking collaboration to create a comprehensive Excel table detailing the LOEUF (Loss-of-Function Observed/Expected Upper Bound Fraction) for each gene, a crucial metric for understanding genetic variations and their implications on health. LOEUF provides insights into genetic variability, aids in understanding disease mechanisms by identifying genes intolerant to loss-of-function mutations, and guides genetic research towards significant biological interests. Our goal is to compile this data into an easy-to-navigate Excel table to be shared on GitHub, promoting open science and collaboration. We're looking for volunteers with expertise in data analysis, genetics, bioinformatics, and Excel to join this project. This is an opportunity to contribute to a community effort in making genetic data accessible and to enhance our understanding of the human genome. If you're interested in contributing or have insights to share, please reach out. Let's collaborate to unlock the secrets of our genome together.
Take https://gnomad.broadinstitute.org/gene/ENSG00000169174 as an example, LOEUF=1.25
0
Entering edit mode
- R/python script to extract Subcellular locations (Compartments) from Genecards?
- Tissue specific mRNA expression dataset in human and mouse
- Mathematical/Statistical models to predict mRNA half-life
- Receptors with internalization capability
- rsq Filter in Michigan imputation Server
- fastq-dump split-spot and skip-technical
- Awk in Bioinformatics
- Gallery: Computational tools for DNA methylation
- Server Vendors to provide bioinformatics talents
- "moving average" function for "coverage" signal in bed files?
- eagle2 + minimac4 script for phasing and imputation
- How to understand Structural Variation in bedpe format?
- Genetic variation calling (SNPs) from bulk RNA-seq dataset
- Consensus genotype of MUTECT1, MUTECT2, Varscan, Muse and Somaticsniper
- How to download GTEx figure from USCS genome browser
- Human tissue expression dataset except GTEx
- How to download dbSNP153 vcf files in hg19/GRCH37 version
- ChEMBL ID to Ensembl ID
- eQTL Catalogue Browser: limitation
- Apply beagle5.0 to make imputation and phasing under CentOS and PBS
- Phenotype Enrichment Analysis vs Gene Enrichment Analysis
- Instrumental Variables and confounder in Mendelian Randomization
- Formula of LOEUF: loss-of-function observed/expected upper bound fraction
- Individual-level data for Million Veteran Program (MVP)
- EGAD00010001497 vs EGAD00010001474
- ICD10, main ICD10 and secondary ICD10
- Structural Variation data of ICGC/PCAWG: 2,658 cancers across 38 tumour types
- Script to obtain human protein sequences by the gene symbols
- Command to download "Height" information from UKB with ukbfetch
- How to understand Instance and Array in UKB phenotype data
- KGML to SBML, BioPax, Sif (XGMML) or PSI-MI
- Roadmap Epigenomics Project Sample Amalgamation of Same Tissue?
- meta-analysis to multiple RNA-seq differential studies
- Method to Check Fastq Completeness after Fastq-dump
- bcftools merge 1021 individual vcf files
- Slurm, Son of Grid Engine, Mesos, and Hadoop YARN vs HTCondor and Torque
- Pros and cons to do biomedical research in pharmaceutical company
- Hg19 regions for Intergenic, Promoters, Enhancer, Exon, Intron, 5-UTR, 3-UTR and so on
- Zn binding sites and active site location in conserved domain database (CDD)
- Script to download fasta seqeuences for FGF1 to FGF12
- How to decrease the number of candidate TFs binding to gene promoter region
- Toxicity genes in metagenome RNA-seq data
- Handbooks for Bioinformatics Ninjas
- RNA-seq data including mixture samples like human, virus, bacterials
- Standard pipeline for drug target discovery and identification
- GTF annotation for Staphylococcus aureus
- Pan-cancer dataset of GENIE control data download and sharing
- Limitation of UKBB genotyping/sequencing data in drug target identificantion
- a gene become a drug target
- benefit of transfering hg19 vcf to hg38 vcf
- novel approaches to the functional assessment of genomic and/or epigenomic variants
- Linux sort P-values with scientific notation
- How to identify similar scientists based on published abstracts
- Detecting copy number variants from whole-exome sequencing data
- How to do data cleaning for VCF genetic file
- Phylogenetic tree with 0,1 matrix as the input?
- How to identify Transcript Factors (TF) binding to my target sequence
- lncRNA and mRNA regulation network database
- Hapmap3 in hg19/GRCh37 plink format PED and MAP
- beagle running error: Insufficient space for shared memory file
- IMPACT rating in VEP and compatibility with which tools?
- snpEff: Fatal error reading file the input VCF files and stop runing
- database for putative human loss-of-function variants
- Protocol to process TCGA image data (SVS format): diagnostic or slides
- Software and algorithm for identification of tissue-specific express genes
- Y-DNA and mtDNA Haplogroup Predictor
- Which is better: webgestalt vs david?
- MAGI, cBioPortal, GATK, Genepattern, MuTect, Oncotater, MutSigCV
- bcftools query missense_variant SNPs from gnomad VCF files
- R: heatmap for triangular matrix
- GWAS data analysis strategy or pipeline
- Protocol To Downlad TCGA Data From GDC
- Perl/Python script: phased vcf to phased tped
- Most important International Big Data Projects: Genetics and Epigenetics
- Significant Difference of the File Size between csorted and nsorted BAM file
- lincRNA analysis pipeline and relevant database
- Plink command to find tag SNP for DRB1*01, DRB1*04, and DRB1*10
- Perl/Python script for batch download mRNA sequences for multiple genes
- Single-end vs Pair-end RRBS methyation sequencing
- BAM files for RRBS data in ENCODE Project
- fastq-dump download pair-end fastq without split-files
- GWAS summary file including risk allele, protective allele and disease
- Seed Region Annotation Database for Human miRNA
- Low methylation regions or non-methylation regions from WGBS dataset
- Reference is deletion and negative genomic position label
- Multiplex PCR Primer Design Tools
- Maternal and Paternal Haplogroups Assignment Package
- 1000 Genome Project VCF file and Plink file
- Most Popular and fancy SNP analysis tools Comparison: Plink, SNPassoc, SNPRelate
- Evolution tree with legend figures
- Simulation to analysis nonsynonymous SNV effect to FGF6
- Alternative tools replace MutDB to predict consequences of deleterious SNV
- GTEx Analysis V7 RNA-seq dataset download
- Gdc-client for CentOS 6
- TF motif binding region searching script in human genome
- Methylation 27K 450K, 850K, 2.5M: Why not plant more probes
- How to provide re-analysis link to previous dataset in GEO page
- How to infer the target TF gene of ZNF132 without any ChIP-seq knowledge?
- Fastqc result collection script
- mysql command to download mm9 Mappability tables from Mapping and Sequencing
- Public data access: Single-cell RNA-seq and Bulk RNA-seq data
- bedtools shuffle with adjustment of GC ratio
- Good Habit for Bioinformatics Analyst or Scientist
- The fastest BS-seq data alignment tools and setting
- Segmentation method comparisons: HMM, CBS, RS
- Roadmap WGBS methylation data download
- Blueprint WGBS data explanation
- How to understand the data and the sample for BS-seq data from TCGA
- DataFormat: Methylation : qmap bis-seq format To bigwig/wig/bedgraph
- How to hide UCSC tracks in bigwig setting
- BAM Flag From Bismark Alignment: Forward and Reverse Chain
- R: How to show Correlation matrix as LD blocks similar as in haploview
- Linkage Disequilibrium to Rare SNPs
- HM450K and WGBS data for Same Sample
- TANRIC: lncRNA and methylation interaction
- Genomic Annotation Atlas (Human and Mouse)
- H3K27Ac Mark Atlas in Human Genomes
- How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
- Batch effect of RRBS data (Methylation): Elimination and Pipleline
- What's the difference between EGA, ENA, GEO, SRA and ArrayExpress
- The Best Pipeline for Indel Calling
- Bioinformatic Interpretation of Gene Expression in Genecard
- Bad Exprience on bigwig Format Visualization in UCSC
- Average Methylation Level for a Genomic Region from Bam File (PileOMeth )
- Development Layer Specific Gene Expression Atlas in Human
- Relationship table between SRX and SRR in SRA database
- Processing Order of the trim_galore
- Authoritative genomic regions for Promoter and Enhancer of Human genome
- The Best Abstract Structure
- Cleanadaptors Vs Cutadapt Vs Trim_galore
- Converting Phred64 fastq to Phred33 fastq
- Baby feature prediction based on genome and phenotype of parents.
- The best data format for to store BS-seq or RRBS dataset
- DNA sequence origin mapping [blast]
- Bismark bug in BS-seq alignment
- Fa list for illumina sequencing adapters
- trim_galore and cutadapt to paired-end DNA sequencing
- Methylation Bisulfite-Sequencing: Bismark, BS seeker, BSMAP, RMAPBS, MAQ
- Methylation, Bisulfite sequencing: Reads, Alignment and Samtools tview
- Bisulfite Sequencing Alignment: SOAP, BOWTIE2, BWA, LAST, GEM
- R: extract interest nucleotide from BAM files (BS-Seq)
- Fold change > 2 and P-value<0.05 in micro-array differential analysis
- R: Difference between heatmap, heatmap.plus and heatmap.2
- Normalization of BS-seq data between different batches
- The best definition to Enhancer and Promoter?
ADD REPLY
• link
25 days ago by
Pierre Lindenbaum
161k
