...
| Software | Description |
|---|---|
| scons | Software build tool |
| swig | Software development tool |
| sqlite3 | SQL Lite databases |
| git | Version control utilities |
Additional Python Tools (cqb-devel_tools/manifests/python.pp)
| Software | Description | in devel_tools |
|---|---|---|
| all-dev | y | |
| blaze | An interface to query data on different storage systems | y |
| cutadapt | Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads | y |
| dendropy | phylogenetic computing | y |
| freetype-dev (libfreetype6-dev) | y | |
| leukgen-disambiguate | y | |
| MACS2 | Model Based Analysis for ChIP-Seq data | y |
| maplot | y | |
| matplotlib | python 2D plotting library | y |
| networkx | Creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | y |
| nimfa | Nonnegative matrix factorization | y |
| numpy | scientific computing with Python | y |
| pandas | Python Data Analysis Library | y |
| patsy | y | |
| pip | Python installation program (to install python modules) | y |
| plotly | y | |
| pysam | y | |
| pyvttbl | y | |
| reportlab (->biopython?) | y | |
| rpy2 | Python interface to R | y |
| seaborn | y | |
| scipy | Collection of Python software for mathematics, science, and engineering. | y |
| sklearn | Machine Learning in Python | y |
| skimage | Image processing in Python | y |
| statsmodels | Estimation of statistical models | y |
Additional R Tools (
...
cqbhiera/common.yaml)
| Software | Description | in common.yaml | |
|---|---|---|---|
| abind | GNU R package “Combine multi-dimensional arrays” | y | |
ade4 | GNU R package “Analysis of Ecological Data : Exploratory | ||
| ape | GNU R package “Analyses of Phylogenetics and Evolution” | ||
bitops | GNU R package implementing bitwise operations | ||
catools | GNU R package “Tools: moving window statistics, GIF, | ||
| cargo | y | ||
cluster | GNU R package for cluster analysis by Rousseeuw et al | ||
| cowplot | |||
| curl | y | ||
data.table | GNU R package “Extension of data.frame” | ||
dbi | GNU R package “R Database Interface” | ||
| dbplyr | y | ||
| dendextend | |||
dichromat | Color schemes for dichromats | ||
digest | GNU R package “Create Cryptographic Hash Digests of R | ||
evaluate | GNU R package “Parsing and Evaluation Tools that Provide | ||
| forcats | y | ||
| foreach | y | ||
futile.logger | GNU R package “A Logging Utility for R” | ||
futile.options | GNU R package “Futile options management” | ||
gdata | GNU R package “Various R Programming Tools for Data | ||
getopt | GNU R package “C-like getopt behavior.” | ||
| gganimate | y | ||
| GGally | y | ||
ggplot2 | GNU R package “An Implementation of the Grammar of | ||
| ggpubr | |||
| ggrepel | y | ||
| gifski | y | ||
gplots | GNU R package “Various R Programming Tools for Plotting | ||
| gridSVG | |||
gtable | GNU R package “Arrange grobs in tables.” | ||
gtools | GNU R package “Various R Programming Tools” | ||
| haven | y | ||
| igraph | y | ||
| interactions | y | ||
| jpeg | y | ||
labeling | GNU R package “Axis Labeling” | ||
lambda.r | GNU R package “Modeling Data with Functional Programming” | ||
lattice | GNU R package “Lattice Graphics” | ||
| leaps | GNU R package “regression subset selection” | lme4 | GNU R package y |
| libssl-dev | prereq? | y | |
| libcairo2-dev | perreq? | y | |
| libxt-dev | prereq? | y | |
| libgmp10 | prereq? | y | |
| libgmp-dev | prereq? | y | |
| libmpfr6 | prereq? | y | |
| libmpfr-dev | prereq? | y | |
| lme4 | GNU R package for linear mixed effects model fitting | y | |
| lubridate | y | ||
matrix | GNU R package of classes for dense and sparse matrices | ||
matrixstats | R package “Methods that apply to rows and columns of a matrix” | ||
| mirbase.db | |||
| mixdist | y | ||
| modelr | y | ||
| multcomp | |||
munsell | GNU R package “Munsell colour system” | ||
| mvtnorm | |||
| network | y | ||
nlme | GNU R package for (non-)linear mixed effects models | ||
| ontologyIndex | y | ||
optparse | GNU R package “Command line option parser.” | ||
permute | GNU R package “Functions for Generating Restricted | ||
| pheatmap | y | ||
| plotly | y | ||
| plotROC | y | ||
| plotrix | GNU R package “Various plotting functions” | y | |
plyr | GNU R package “Tools for Splitting, Applying and Combining | ||
proto | GNU R package “Prototype object-based programming” | y | |
| quantmod | y | ||
r.methodss3 | GNU R package “Utility function for defining S3 methods” | ||
rcolorbrewer | GNU R package providing suitable color palettes | ||
rcpp | GNU R package “Seamless R and C++ Integration” | ||
rcurl | GNU R package “General Network (HTTP/FTP/…) Client | ||
relimp | GNU R package “Relative Contribution of Effects in a | y | |
reshape2 | GNU R package “Flexibly Reshape Data: A Reboot of the | y | |
| reticulate | y | ||
rggobi | GNU R package for the GGobi data visualization system | y | |
rgl | GNU R package for three-dimensional visualisation using OpenGL | ||
rgtk2 | GNU R binding for Gtk2 | ||
rmpi | GNU R package interfacing MPI libraries for distributed computing | y | |
| RMySQL | y | ||
rserve | GNU R Rserve tcp/ip server and sample clients | y | |
rsqlite | GNU R package “SQLite Interface for R” | ||
| rvest | y | ||
scales | GNU R package “Scale Functions for Visualization” | ||
scatterplot3d | GNU R package “3D Scatter Plot” | y | |
| Seurat | y | ||
| shiny | y | ||
| sna | y | ||
sp | GNU R package “Classes and Methods for Spatial Data” | ||
| sqldf | y | ||
stringr | GNU R package “Simple, Consistent Wrappers for Common | ||
tcltk2 | GNU R package “Tcl/Tk Additions” | y | |
testthat | GNU R package “Testthat code. Tools to make testing fun | ||
| tibble | y | ||
| tidyr | y | ||
| tidyverse | y | ||
| transformr | y | ||
vegan | GNU R package “Community Ecology Package” | ||
| VennDiagram | y | ||
| VGAM | y | ||
| vioplot | y | ||
xml | GNU R package “Tools for Parsing and Generating XML Within | ||
xtable | GNU R coerce data to LaTeX and HTML tables |
Additional R BioConductor Tools (
...
cqbhiera/common.yaml)
| Software | Description | |
|---|---|---|
| affy | y | |
| affyio | GNU R package “Tools for parsing Affymetrix data files” | |
| annotate | GNU R package “Annotation for microarrays” | |
annotationdbi | GNU R package “Annotation Database Interface” | |
| arrayQualityMetrics | ||
| ballgown | Flexible, isoform-level differential expression analysis | |
| biobase | GNU R package “Biobase: Base functions for Bioconductor” | |
biocgenerics | GNU R package “S4 generic functions for Bioconductor” | |
biocinstaller | GNU R package “Install/Update Bioconductor and CRAN | |
biocparallel | GNU R package “Bioconductor facilities for parallel | |
biomart | GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene) | |
biostrings | GNU R package “String objects representing biological | |
| BSgenome | Efficient genome searching | |
| BSgenome.Hsapiens.UCSC.hg19 | ||
| ChIPseeker | annotating ChIP-seq data analysis | |
| cummeRbund | analyzing Cufflinks RNA-Seq output | |
| deseq | ||
| DESeq2 | Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution | |
| devtools | Collection of package development tools | |
| DEXSeq | finding differential exon usage using RNA-seq exon counts between samples | |
| genfilter | GNU R package “genefilter: methods for filtering genes | |
geneplotter | Graphics related functions for Bioconductor | |
genomeinfodb | GNU R package “Utilities for manipulating chromosome and | |
genomicalignments | GNU R package “Representation and manipulation of short | |
genomicranges | GNU R package “Representation and manipulation of genomic | |
| GISPA | ||
| GOstats | tools for interacting with GO and microarray data | |
| GO.db | ||
hilbertvis | GNU R package to visualise long vector data | |
iranges | GNU R package “Infrastructure for manipulating intervals | |
| JunctionSeq | ||
limma | GNU R package “Linear Models for Microarray Data” | |
| mirbase.db | ||
multtest | GNU R package “Resampling-based multiple hypothesis | |
| org.Sc.sgd.db | ||
| org.Mm.eg.db | ||
preprocesscore | GNU R package “A collection of pre-processing functions” | |
| qvalue | Bioconductor package “Q-value estimation for false discovery rate control” | |
| rhdf5 | provides an interface between HDF5 and R | |
| readr | ||
| ReportingTools | ||
| RIPSeeker | identify protein-associated transcripts from RIP-seq experiments | |
| rsamtools | GNU R package “Binary alignment (BAM), variant call (BCF), | |
s4vectors | GNU R package “S4 implementation of vectors and lists” | |
| SISPA | ||
| sleuth | analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto | |
| ShortRead | sampling, iteration, and input of FASTQ files | |
| topGO | ||
| TxDb.Scerevisiae.UCSC.sacCer3.sgdGene | ||
| TxDb.Hsapiens.UCSC.hg38.knownGene | ||
| tximport | ||
| WGCNA | ||
xvector | GNU R package “Representation and manpulation of external | |
zlibbioc | GNU R package “An R packaged zlib-1.2.5″ |
...