kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
kallisto is a program for quantify...pts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput s.... On benchmarks with standard RNA-Seq data, kallisto can...sp;Near-optimal probabilistic RNA-seq quantification, Nature Biotec...1937 days ago
1937 days ago
ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment
ChIP-seq simulation pipeline, ChIPulate, we assess the impact of various biological and experimental sources of variation on several outcomes of a ChIP-seq experiment, viz., the recover...1860 days ago
1775 days ago
Snakemake workflow: dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.1738 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as woul...1624 days ago
Seq: A high-performance, Pythonic language for bioinformatics
Seq is a programming language for computational genomics and bioinformatics. With...on-compatible syntax and a host of domain-specific features and optimizations, Seq makes writing high-performanc...1617 days ago
BioJupies: Automatically Generates RNA-seq Data Analysis Notebooks
With BioJupies you can produce in seconds a customized, re...nteractive report from your own raw or processed RNA-seq data through a simple user in...page for access to unlimited private notebooks, RNA-seq datasets and alignment jobs....1224 days ago
StringTie Transcript assembly and quantification for RNA-Seq
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It...assemblers, but also alignments of longer sequences that have been assemble...n, Cuffdiff or other programs (DESeq2, edgeR, etc.).1418 days ago
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
Rcorrector has an accuracy higher than or co...other method (SEECER) designed for RNA-seq reads, and is more time and m...pl [OPTIONS] OPTIONS: Required -s seq_files: comma separated files...mate in the paried-end data sets -2 seq_files_right: comma separated...1543 days ago