SpotSweeper – spatially aware quality control for spatial transcriptomics
As scientists explore how genes are expressed in different parts of tissues, they increasingly rely…
Browsing: Quality Control
RNA-seq validation – software for selection of reference and variable candidate genes for RT-qPCR
Introduction to RT-qPCR Real-time quantitative PCR (RT-qPCR) is a powerful tool used by scientists to…
PARE – a framework for removal of confounding effects from any distance-based dimension reduction method
Imagine you have a complex dataset with lots of dimensions, like a massive library of…
Splice_sim – a nucleotide conversion-enabled RNA-seq simulation and evaluation framework
RNA plays a crucial role in all living cells, acting as a messenger that carries…
FindAdapt – A python package for fast and accurate adapter detection in small RNA sequencing
Adapter trimming is an essential step for analyzing small RNA sequencing data, where reads are…
scReadSim – a single-cell RNA-seq and ATAC-seq read simulator
Benchmarking single-cell RNA-seq (scRNA-seq) and single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) computational tools…
The Dex-Benchmark resource – datasets and code to evaluate algorithms for transcriptomics data analysis
Many tools and algorithms are available for analyzing transcriptomics data. These include algorithms for performing…
RNA Strain-Match – a tool for matching single-nucleus, single-cell, or bulk RNA-sequencing alignment data to its corresponding genotype
When next generation sequencing is performed in large batches, there are several stages at which…
SoCube – an innovative end-to-end doublet detection algorithm for analyzing scRNA-seq data
Doublets formed during single-cell RNA sequencing (scRNA-seq) severely affect downstream studies, such as differentially expressed…
SAMStat 2 – quality control for next generation sequencing data
SAMStat is an efficient program to extract quality control metrics from fastq and SAM/BAM files.…