Reverse Dependencies of pysam
The following projects have a declared dependency on pysam:
- ScaleHD — Automated DNA micro-satellite genotyping.
- ScaleHD-ALSPAC — Automated DNA micro-satellite genotyping.
- scAllele — A versatile tool for the detection and analysis of nucleotide variants in scRNA-seq
- ScanCE — A computational workflow for cryptic exon identification in RNA-seq data.
- scanexitronlr — ScanExitronLR: a lightweight tool for the characterization and quantification of exitrons in long read RNA-seq data
- scape-apa — A package for estimating alternative polyadenylation events from scRNA-seq data.
- scdna-replication-tools — Code for analyzing single-cell replication dynamics
- scgenome — Code for analyzing single cell whole genomes
- schickit — a toolkit for processing single cell Hi-C data
- scikit-ribo — A scikit framework for joint analysis of Riboseq and RNAseq data
- sctools — Utilities for large-scale distributed single cell data processing
- scutls — Single-cell data processing utility tools
- scverse — scverse bundle
- searcHPV — An HPV integration sites detection tool for targeted capture sequencing data
- seqchromloader — Sequence and chromatin dataloader for deep learning
- seqdata — Annotated sequence data
- seqlib — provide an in-memory interface to bwa mem
- seqpandas — Read bioinformatics sequence formats into a Pandas DataFrame
- sequana — A set of standalone application and pipelines dedicated to NGS analysis
- sequence-qc — Package for doing various ad-hoc quality control steps from MSK-ACCESS generated FASTQ or BAM files
- SIDR — Sequence Idenification using Decision tRees; a tool to classify DNA reads using machine learning models.
- simplebitk — A bioinformatics tools kit
- singlecellmultiomics — Tools to deal with one or more measurements from single cells
- sinto — Tools for single-cell data processing
- SIRVsuite — SIRVsuite - a command line tool to QC an RNA-Seq workflow using Lexogen's SIRV spike-in controls
- slamdunk — SLAMdunk suite for analyzing SLAM-seq data
- sma-finder — A tool for diagnosing spinal muscular atrophy (SMA) using exome or genome sequencing data
- smallgenomeutilities — A collection of scripts that are useful for dealing with viral RNA NGS data.
- smmips — A package to generate QC metrics for smMIP libraries
- smmuty — Utilities for single-cell multi-omics data
- smvplot — smvplot is a cmd line python tool to generate IGV-like screenshots
- sniffles — A fast structural variation caller for long-read sequencing data
- SNPfilter — A handy little tool for filtering SNPs.
- snpio — Reads and writes VCF, PHYLIP, and STRUCTURE files and performs data filtering on the alignment.
- snpToolkit — SNPs filtering, annotation and combining
- snvoter — A top up tool to enhance SNV calling from Nanopore sequencing data.
- sos-bioinfo — SoS Notebook extension for bioinformatics applications
- specivar — Filter VCF to variants that are specific to a sample group
- spectre-cnv — Long read copy number variation (CNV) caller
- spiker — spiker (Analysis workflow for ChIP-seq data with spike-in)
- SPLICE-q — SPLICE-q is a fast and user-friendly Python tool for genome-wide SPLICing Efficiency quantification
- splicekit — splicekit: comprehensive toolkit for splicing analysis from short-read RNA-seq
- SpliceV — Visualize splice junctions, backsplice junctions (circleRNA) and coverage from RNA-Seq datasets
- splitbam — Split a BAM file into two subsamples
- SplitStrains — SplitStrains detects and separates mixed strains of Mycobacterium tuberculosis.
- srslyrun — Not your grandma's NGS analysis - software for analyzing FASTQs from SRSLY libraries
- srslyumi — process SRSLY UMIs
- stepRNA — Align short RNA seqeuncing reads to determine the length of of overhang.
- str-analysis — Utilities for analyzing short tandem repeats (STRs)
- strainge — Strain Genome Explorer: a tool suite for tracking and characterizing low-abundance strains.
- STRcount — A package to count the number of repeats in a Short Tandem Repeat Expansion from long reads.
- strkit — A toolkit for analyzing variation in short(ish) tandem repeats.
- subcellular-sprawl — Subcellular Patterning Ranked Analysis With Labels
- superseal — Reference-guided viral quasipsecies reconstruction
- svim — A structural variant caller for long reads.
- svim-asm — A structural variant caller for genome-genome alignments.
- svtyper — Bayesian genotyper for structural variants
- svviz — A read visualizer for structural variants
- tbpore — Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
- TEcount — Count read alignments on transposable elements subfamilies, families and classes.
- telescope-ngs — Single locus resolution of Transposable ELEment expression using next-generation sequencing.
- telomerecat — Telomere Computational Analysis Tool
- telomerehunter — Estimation of Telomere Content from WGS Data
- TEtranscripts — Tools for estimating differential enrichment of Transposable Elements and other highly repetitive regions
- tigmint — Correct misassemblies using linked reads
- tin-score-calculation — no summary
- tinycov — Standalone command line tool to visualize coverage from a BAM file
- tns-piler — Tool for finding cumulative pileups
- ToolBiox — a biological toolkit for genome assembly, annotation and analysis that we have accumulated from our bioinformatics work
- track-duplicates — A simple tool to extract reads from a certain taxa from BAM files
- trackcluster — RNA-seq analysis for Long read RNA sequencing
- trackplot — The trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets. https://sashimi.readthedocs.io/
- trand — 'Transcript Distances'
- transcov — A software for mapping coverage around transcription start sites
- triplix — A python package to efficiently process, store and retrieve spatial genomics multi-contact data
- TRSalgorithm — Determining 3' termini of transcripts from RNAtag-seq data in bacteria
- trtools — Toolkit for genome-wide analysis of STRs
- Truvari — Structural variant comparison tool for VCFs
- umi_tools — umi_tools: Tools for UMI analyses
- umi-tools-csgx — umi_tools: Tools for UMI analyses
- umierrorcorrect — UMI error correct
- umis — Package for estimating UMI counts in Transcript Tag Counting data.
- umitools — A toolset for handling sequencing data with unique molecular identifiers (UMIs)
- utlts — Utility functions.
- UTRme — UTRme
- vafator — Annotate a VCF file with AF, AD and DP from tumor and normal BAMs
- vamb — Variational autoencoder for metagenomic binning
- var2pharm — End-to-end pharmacogenomics research tool that enables personalized drug dosing based on individual's variants
- VaRaPS — VaRaPS : Variants Ratios from Pooled Sequencing
- varconv — no summary
- variant-extractor — Deterministic and standard extractor of indels, SNVs and structural variants (SVs) from VCF files
- varianteval — Library to help compare VCF files
- variantfinder — python package to scan bam files for alignemnts variants of interest
- variantworks — NVIDIA genomics python libraries and utiliites
- VaSeBuilder — VaSeBuilder, a bioinformatic tool for artificially combining multiple NGS samples into a single, hybrid sample.
- vatools — A tool for annotating VCF files with expression and readcount data
- vcf-annotation-tools — A tool for annotating VCF files with expression and readcount data
- vcf2fhir — Convert .vcf files to HL7 FHIR standard
- vcf2fhir-test-517 — Convert .vcf files to HL7 FHIR standard
- vcf2fhir-test-upgrade-test-upgrade — Convert .vcf files to HL7 FHIR standard