Källkodspaket: bcbio (1.2.9-2)
[contrib]
Länkar för bcbio
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Följande binärpaket byggs från detta källkodspaket:
- bcbio
- toolkit for analysing high-throughput sequencing data
- python3-bcbio
- library for analysing high-throughput sequencing data
Andra paket besläktade med bcbio
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- arkitekturoberoende bygg-beroende
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debhelper-compat
(= 13)
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dh-python
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python3-all
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python3-setuptools
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python3-gffutils
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python3-mock
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python3-pandas
- data structures for "relational" or "labeled" data
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python3-pybedtools
- Python 3 wrapper around BEDTools for bioinformatics work
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- adep:
python3-pysam
- interface for the SAM/BAM sequence alignment and mapping format (Python 3)
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- adep:
python3-pyvcf
- virtuellt paket som tillhandahålls av
python3-vcf
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python3-toolz
- List processing tools and functional utilities
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python3-tornado
- scalable, non-blocking web server and tools - Python 3 package
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python3-yaml
- YAML parser and emitter for Python3
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python3-scipy
- scientific tools for Python 3
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- adep:
python3-psutil
- module providing convenience functions for managing processes (Python3)
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python3-joblib
- tools to provide lightweight pipelining in Python
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atropos
- NGS read trimming tool that is specific, sensitive, and speedy
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- adep:
bcftools
- genomic variant calling and manipulation of VCF/BCF files
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- adep:
bedtools
- suite of utilities for comparing genomic features
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- adep:
biobambam2
- tools for early stage alignment file processing
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- adep:
bowtie2
- ultrafast memory-efficient short read aligner
-
- adep:
bwa
- Burrows-Wheeler Aligner
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- adep:
cnvkit
- Copy number variant detection from targeted DNA sequencing
-
- adep:
fastqc
- quality control for high throughput sequence data
-
- adep:
freebayes
- Bayesian haplotype-based polymorphism discovery and genotyping
-
- adep:
gffread
- GFF/GTF format conversions, region filtering, FASTA sequence extraction
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- adep:
grabix
- wee tool for random access into BGZF files
-
- adep:
gsort
- sort genomic data
-
- adep:
hisat2
- graph-based alignment of short nucleotide reads to many genomes
-
- adep:
hts-nim-tools
- tools biological sequences: bam-filter, count-reads, vcf-check
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- adep:
libfreetype6
- FreeType 2 font engine, shared library files
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- adep:
lumpy-sv
- general probabilistic framework for structural variant discovery
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- adep:
mosdepth
- BAM/CRAM depth calculation biological sequencing
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- adep:
multiqc
- output integration for RNA sequencing across tools and samples
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- adep:
perl
- Larry Wall's Practical Extraction and Report Language
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- adep:
libpicard-java
- Java library to manipulate SAM and BAM files
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- adep:
libvcflib-tools
- C++ library for parsing and manipulating VCF files (tools)
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- adep:
picard-tools
- Command line tools to manipulate SAM and BAM files
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- adep:
python3-biopython
- Python3 library for bioinformatics
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- adep:
python3-cyvcf2
- VCF parser based on htslib (Python 3)
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- adep:
python3-geneimpacts
- wraps command line tools to assess variants in gene sequences
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- adep:
python3-logbook
- logging system for Python that replaces the standard library's module (Python 3)
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- adep:
python3-nose
- test discovery and running for Python3 unittest
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- adep:
python3-requests
- elegant and simple HTTP library for Python3, built for human beings
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- adep:
python3-pytest
- Simple, powerful testing in Python3
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- adep:
python3-pytest-mock
- Thin wrapper around mock for easier use with pytest (Python 3 module)
-
- adep:
python3-seqcluster
- analysis of small RNA in NGS data
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- adep:
pythonpy
- 'python -c', with tab completion and shorthand
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- adep:
rapmap
- rapid sensitive and accurate DNA read mapping via quasi-mapping
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- adep:
rna-star
- ultrafast universal RNA-seq aligner
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- adep:
r-base-core
- GNU R core of statistical computation and graphics system
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- adep:
r-bioc-htsfilter
- GNU R filter replicated high-throughput transcriptome sequencing data
-
- adep:
r-bioc-degreport
- BioConductor report of DEG analysis
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- adep:
r-bioc-purecn
- copy number calling and SNV classification using targeted short read sequencing
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- adep:
r-bioc-summarizedexperiment
- BioConductor assay container
-
- adep:
r-cran-tidyverse
- Easily Install and Load the 'Tidyverse'
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- adep:
r-bioc-titancna
- Subclonal copy number and LOH prediction from whole genome sequencing
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- adep:
r-bioc-tximport
- transcript-level estimates for biological sequencing
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- adep:
r-other-wasabi
- prepare Sailfish and Salmon output for downstream analysis using GNU R
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- adep:
salmon
- wicked-fast transcript quantification from RNA-seq data
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- adep:
samblaster
- marks duplicates, extracts discordant/split reads
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- adep:
samtools
- processing sequence alignments in SAM, BAM and CRAM formats
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- adep:
seqan-apps
- C++ library for the analysis of biological sequences
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- adep:
seqtk
- Fast and lightweight tool for processing sequences in the FASTA or FASTQ format
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- adep:
snpeff
- genetic variant annotation and effect prediction toolbox - tool
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- adep:
subread
- toolkit for processing next-gen sequencing data
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- adep:
tabix
- generic indexer for TAB-delimited genome position files
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- adep:
tophat-recondition
- post-processor for TopHat unmapped reads
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- adep:
umis
- tools for processing UMI RNA-tag data
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- adep:
vcfanno
- annotate a VCF with other VCFs/BEDs/tabixed files
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- adep:
vt
- toolset for short variant discovery in genetic sequence data
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- adep:
wham-align
- Wisconsin's High-Throughput Alignment Method
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- adep:
xonsh
- Python-powered, cross-platform, Unix-gazing shell
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- adep:
libhts-dev
- development files for the HTSlib
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- adep:
python3-sphinx
- documentation generator for Python projects
