wyang17 / SQuIRE
Software for Quantifying Interspersed Repeat Expression
☆55Updated 2 years ago
Alternatives and similar repositories for SQuIRE:
Users that are interested in SQuIRE are comparing it to the libraries listed below
- A package for quantifying transposable elements at a locus level for RNAseq datasets.☆26Updated 3 months ago
- Allele-specific alignment sorting☆55Updated 2 years ago
- Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…☆73Updated 2 years ago
- ☆61Updated 9 months ago
- ENCODE long read RNA-seq pipeline☆47Updated 2 years ago
- ☆58Updated 3 years ago
- A Perl/R pipeline for plotting metagenes☆37Updated 3 years ago
- Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics☆110Updated 2 weeks ago
- optimization of ribosome P-site positioning in ribosome profiling data☆52Updated 2 months ago
- TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C☆107Updated 4 years ago
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆66Updated 5 years ago
- Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome☆69Updated last year
- Long-read Isoform Quantification and Analysis☆39Updated last month
- Publication quality NGS track plotting☆111Updated 2 years ago
- trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and fu…☆89Updated last month
- SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3☆38Updated 4 years ago
- Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…☆85Updated 2 years ago
- HiC uniform processing pipeline☆59Updated last year
- Somatic structural variant caller for long-read data☆65Updated last week
- Estimate locus specific human LINE-1 expression.☆34Updated 2 years ago
- SingleCell Nanopore sequencing data analysis☆58Updated 4 months ago
- EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2☆60Updated 6 months ago
- FEELnc : FlExible Extraction of LncRNA☆87Updated 7 months ago
- Quantification of transposable element expression using RNA-seq☆68Updated last year
- Variant Calling Pipeline Using GATK4 and Nextflow☆54Updated 2 years ago
- An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)☆112Updated 3 months ago
- fork of RSeQC python RNAseq metrics suit of tools☆48Updated 6 years ago
- RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.☆39Updated 3 years ago
- toolbox for analysing BS-seq data, advance features in SNV, ASM and DMR☆62Updated last year
- Snakemake-based workflow for detecting structural variants in genomic data☆80Updated 2 months ago