Bioinformatic Tools¶
- Predicting in vivo TFBS using Catchitt
- Calling significant interactions from Capture-C or Capture-HiC
- GSEA and pathway/GO enrichment analyses
- Replicate correlation and QC for HiC data
- Gene expression clustering
- Consensus peaks given multiple (>=2) replicates
- NCBI data submission
- Local UCSC cell browser usage for Seurat
- notes on alphafold
- Assigning features to a bed file.
- General bait design
- calculate chrM percent
- Filter bam files and generate bw files
- check sample barcode frequency in index reads
- Barcode frequency in 5’-end
- Download raw data from Illumina Base Space
- Convert BCL basecall files to FASTQ files
- BedGraph to BigWiggle
- bed overlap bedpe
- Query bed overlap with a list of bed files
- Merging bigwiggle files into one bw
- Input
- Usage
- Chromatin interaction calling in captureC data
- ATAC-seq model and footprint prediction using Chrombpnet
- Summary
- Input
- Important note
- Usage
- Output
- QC
- Visualize genomic loci (overview)
- Count indel integration pipeline
- Count indel integration pipeline (simplified version)
- Crispresso2 for HDR
- Convert CRISPResso allele frequency table to vcf-like table
- Interactive visualization using Dash Bio
- convert dataframe to html
- CRISPR Screening Demultiplexing
- CRISPR Screening Demultiplexing (hard trim first N random bp)
- Demultiplexing fastq files
- Diff or merge of two bw files
- DNAnexus download and upload
- EGACryptor for EGA submission
- Call interactions from HiC
- Extract inward/outward oriented pairs from BAM file
- Merge fastq I1 I2 R1 R2 reads into R1 and R2
- subsample fastq and visualize in sequence logo
- Run fastQC for a list of fastq files
- Filter out reads mapped to specific sequences
- Annotate vcf file (custom annotation not work)
- Genomic features annotatoin given bed file
- Extract user-defined gene promoter from refseq TSS database
- Find allele (e.g., SNPs) specific effects
- Integrating gene expression data and PPI network
- Objective
- Steps
- Cons
- Input
- Usage
- Output
- GTF operations
- Running GUIDE-seq in HPC
- HiC-Pro
- Generate indexed genome, chrom size, and res fragment bed for HicPro analysis
- Homer ChIP-seq analysis
- How to download all files from a website
- ENCODE database query
- Transcript-level abundance quantification
- Kmer count over bed
- Lift Over Bed or bigWiggle files
- LiftOverVCF
- Seurat to Loupe browser
- Merge multiple bedfiles
- Merge fastq files for L001 L002 L003 L004
- Write flowchart using text
- Using nf-core pipelines on HPC
- OnTAD
- Optimal subset finding problem in mutagenesis studies
- Filtering out peaks in narrowPeak files
- Convert rmd to html
- RNA-seq QC
- Across cell type NGS data normalization
- single cell RNA-seq data integration
- FASTQ files operations
- Smoothing a bedgraph file
- Download fastq data from NCBI SRA
- Subsample fastq to the same sequencing depth
- Super-enhancer identification
- Convert a column to bigwiggle file
- Using GPU on HPC
- Test differences in number of interactions
- Identify direct targets and co-binding factors
- Extract Ensembl Gene Name and IDs given IDs or names from any databases
- (TOBIAS) Footprint analysis for ATAC-seq data
- Uditas
- Generate new genome given vcf file