云服务器使用

生信服务器预装软件

开箱即用的生信分析环境：内置数十款常用生信软件与 1000+ R 语言分析包，上机即可开展分析。(有额外的软件需求，直接呼叫技术部署即可)

常用生信软件

SRA Toolkit

版本未指定

用途：测序数据下载

安装方式：APT

版本检查：fasterq-dump --version

FastQC

v0.12.1

用途：原始测序数据质控

安装方式：解压+软链接

版本检查：fastqc --version

BEDTools

v2.31.1

用途：基因组区间处理

安装方式：源码编译

版本检查：bedtools --version

BWA

v0.7.18

用途：短序列比对

安装方式：源码编译+软链接

版本检查：bwa 2>&1 | head

gffread

v0.12.7

用途：GFF/GTF 文件处理

安装方式：解压+软链接

版本检查：gffread --version

SAMtools

v1.21

用途：SAM/BAM/CRAM 处理

安装方式：源码编译

版本检查：samtools --version

SeqKit

版本未指定

用途：FASTA/FASTQ 处理

安装方式：解压+软链接

版本检查：seqkit version

STAR

v2.7.11b

用途：RNA-seq 比对

安装方式：解压+软链接

版本检查：STAR --version

Cell Ranger

v9.0.0

用途：单细胞转录组分析

安装方式：解压+软链接

版本检查：cellranger --version

Cell Ranger ATAC

v2.1.0

用途：单细胞 ATAC-seq 分析

安装方式：解压+软链接

版本检查：cellranger-atac --version

Space Ranger

v3.1.2

用途：空间转录组分析

安装方式：解压+软链接

版本检查：spaceranger --version

RStudio Server

版本未指定

用途：R Web IDE

安装方式：DEB/APT

版本检查：rstudio-server version

JupyterHub

版本未指定

用途：多用户 Jupyter 服务

安装方式：pip/npm

版本检查：jupyterhub --version

预装 R 分析包

涵盖 Bioconductor 与 CRAN 常用生信分析包，登录服务器即可 library() 调用。

abind1.4-8

alabaster.base1.8.1

alabaster.ranges1.8.0

alabaster.schemas1.8.0

ALL1.50.0

alphahull2.5

annotate1.86.1

AnnotationDbi1.70.0

AnnotationFilter1.32.0

AnnotationHub3.16.1

ape5.8-1

aplot0.2.8

argparse2.2.5

arrangements1.1.9

arrow21.0.0

askpass1.2.1

assertthat0.2.1

assorthead1.2.0

attempt0.3.1

AUCell1.30.1

autoReg0.3.4

babelgene22.9

backports1.5.0

base4.5.1

base64enc0.1-3

batchelor1.24.0

BayesPrism2.2.3

BBmisc1.13

bcellViper1.44.0

beachmat2.24.0

beeswarm0.4.0

benchmarkme1.0.8

benchmarkmeData1.0.4

BH1.87.0-1

BiasedUrn2.0.12

bibliometrix5.1.0

bibliometrixData0.3.0

bigD0.3.1

biglm0.9-3

BingleSeq0.3.6

Biobase2.68.0

BiocFileCache2.16.1

BiocGenerics0.54.0

BiocIO1.18.0

biocmake1.0.1

BiocManager1.30.26

BiocNeighbors2.2.0

BiocParallel1.42.1

BiocSingular1.24.0

BiocVersion3.21.1

biocViews1.76.0

bioDist1.80.0

biomaRt2.64.0

biomod24.2-6-2

Biostrings2.76.0

bit4.6.0

bit644.6.0-1

bitops1.0-9

blob1.2.4

bluster1.18.0

boot1.3-31

BPCells0.3.0

brew1.0-10

brio1.1.5

broom1.0.9

BSgenome1.76.0

bslib0.9.0

ca0.71.1

cachem1.1.0

Cairo1.6-2

callr3.7.6

car3.1-3

CARD1.1

carData3.0-5

cards0.7.0

cardx0.3.0

caret7.0-1

caretEnsemble4.0.1

catboost1.2.8

caTools1.18.3

CellChat2.1.2

cellranger1.1.0

checkmate2.3.2

CHETAH1.24.0

circlize0.4.16

Ckmeans.1d.dp4.3.5

class7.3-23

classInt0.4-11

cli3.6.5

clipr0.8.0

clock0.7.3

clue0.3-66

cluster2.1.8.1

ClusterGVis0.1.4

clusterProfiler4.16.0

clustree0.5.1

cmprsk2.2-12

CNEr1.43.0

coda0.19-4.1

codetools0.2-20

coin1.4-3

colorRamp20.1.0

colorRamps2.3.4

colorspace2.1-1

combinat0.0-8

commonmark2.0.0

compiler4.5.1

ComplexHeatmap2.24.1

CompQuadForm1.4.4

concaveman1.1.0

config0.3.2

conflicted1.2.0

ConsensusClusterPlus1.72.0

copykat1.1.0

coro1.1.0

corrplot0.95

cowplot1.2.0

cpp110.5.2

crayon1.5.3

credentials2.0.2

crosstalk1.2.1

crul1.6.0

curl6.4.0

CytoTRACE21.1.0

dada21.36.0

data.table1.17.8

data.tree1.1.0

datasets4.5.1

datawizard1.2.0

DBI1.2.3

dbplyr2.5.0

dbscan1.2.2

DDRTree0.1.5

decoupleR2.14.0

DelayedArray0.34.1

DelayedMatrixStats1.30.0

deldir2.0-4

dendextend1.19.1

dendsort0.3.4

DEoptimR1.1-4

Deriv4.2.0

desc1.4.3

DescTools0.99.60

DESeq21.48.1

devtools2.4.5

diagram1.6.5

DiagrammeR1.0.11

DiceKriging1.6.0

diffobj0.3.6

digest0.6.37

dimensionsR0.0.3

diptest0.77-1

dir.expiry1.16.0

DirichletMultinomial1.50.0

dismo1.3-16

distillery1.2-2

dlm1.1-6.1

doBy4.7.0

docopt0.7.2

doParallel1.0.17

doRNG1.8.6.2

dorothea1.20.0

DOSE4.2.0

doSNOW1.0.20

dotCall641.2

DoubletFinder2.0.4

downlit0.4.4

dplyr1.1.4

dqrng0.4.1

DR.SC3.5

drat0.2.5

DT0.33

dtplyr1.3.1

dynamicTreeCut1.63-1

DynDoc1.86.0

e10711.7-16

easybio1.1.1

EBImage4.50.0

edgeR4.6.3

ellipse0.5.0

ellipsis0.3.2

emmeans1.11.2

emoa0.5-3

enrichplot1.28.4

enrichR3.4

ensembldb2.32.0

ensemblVEP1.46.0

estimability1.5.1

evaluate1.0.4

Exact3.3

exactRankTests0.8-35

ExperimentHub2.16.1

expm1.0-0

extRemes2.2-1

factoextra1.0.7

FactoMineR2.12

fansi1.0.6

farver2.1.2

fastcluster1.3.0

fastDummies1.7.5

fastICA1.2-7

fastmap1.2.0

fastmatch1.1-6

fastshap0.1.1

fdrtool1.2.18

fftwtools0.9-11

fgsea1.34.2

fields16.3.1

filelock1.0.3

findpython1.0.9

fitdistrplus1.2-4

flashClust1.01-2

flexmix2.3-20

flextable0.9.10

FNN1.1.4.1

fontawesome0.5.3

fontBitstreamVera0.1.1

fontLiberation0.1.0

fontquiver0.2.1

forcats1.0.0

foreach1.5.2

foreign0.8-90

formatR1.14

Formula1.2-5

fs1.6.6

furrr0.3.1

futile.logger1.4.3

futile.options1.0.1

future1.67.0

future.apply1.20.0

gargle1.5.2

garnett0.1.24

gbm2.2.2

gdtools0.4.3

genefilter1.90.0

geneLenDataBase1.44.0

GeneOverlap1.44.0

generics0.1.4

genetics.binaRies0.1.2

GENIE31.30.0

GenomeInfoDb1.44.1

GenomeInfoDbData1.2.14

GenomicAlignments1.44.0

GenomicFeatures1.60.0

GenomicRanges1.60.0

geometry0.5.2

geomtextpath0.2.0

GEOquery2.76.0

gert2.1.5

getopt1.20.4

GetoptLong1.0.5

ggalluvial0.12.5

ggbeeswarm0.7.2

ggcorrplot0.1.4.1

ggdendro0.2.0

ggforce0.5.0

ggfun0.2.0

ggh4x0.3.1

gghalves0.1.4

ggiraph0.8.13

ggiraphExtra0.3.0

ggnetwork0.5.13

ggnewscale0.5.2

ggplot23.5.2

ggplotify0.1.2

ggpolypath0.4.0

ggpubr0.6.1

ggraph2.2.1

ggrastr1.0.2

ggrepel0.9.6

ggridges0.5.6

ggsci3.2.0

ggsignif0.6.4

ggtangle0.0.7

ggtext0.1.2

ggtree3.16.3

ggunchull1.0.1

ggvenn0.1.10

gh1.5.0

Giotto4.2.1

GiottoClass0.4.7

GiottoUtils0.2.4

GiottoVisuals0.2.12

GiRaF1.0.1

gitcreds0.1.2

gld2.6.7

glmnet4.1-10

GlobalOptions0.1.2

globals0.18.0

glue1.8.0

gmapR1.48.0

gmp0.7-5

GO.db3.21.0

goftest1.2-3

golem0.5.1

googleAuthR2.0.2

googledrive2.1.1

googlesheets41.1.1

googleVis0.7.3

GOSemSim2.34.0

goseq1.60.0

gower1.0.2

gplots3.2.0

graph1.86.0

graphics4.5.1

graphlayouts1.2.2

grDevices4.5.1

grid4.5.1

gridBase0.4-7

gridExtra2.3

gridGraphics0.5-1

gridSVG1.7-6

gridtext0.1.6

grr0.9.5

GSEABase1.70.0

gson0.1.0

GSVA2.2.0

gt1.0.0

gtable0.3.6

gtools3.9.5

gtsummary2.4.0

gwasglue0.0.0.9000

gwasglue20.0.0.9000

gwasvcf0.1.2

gypsum1.4.0

h5mread1.0.1

hardhat1.4.1

Harman1.36.0

harmony1.2.3

haven2.5.5

HDF5Array1.36.0

hdf5r1.3.12

hdWGCNA0.4.05

here1.0.1

hexbin1.28.5

HiClimR2.2.1

HiddenMarkov1.8-14

highr0.11

Hmisc5.2-3

hms1.1.3

hocuspocus1.2.1

hoodscanR1.6.0

HSMMSingleCell1.28.0

htmlTable2.4.3

htmltools0.5.8.1

htmlwidgets1.6.4

httpcode0.3.1.91

httpuv1.6.16

httr1.4.7

httr21.2.1

hwriter1.3.2.1

ica1.0-3

ids1.0.1

ieugwasr1.1.0

igraph2.1.4

iml0.11.4

impute1.82.0

infercnv1.24.0

ini0.3.1

insight1.3.1

interp1.1-6

intervals0.15.5

intrinsicDimension1.2.0

iotools0.3-5

ipred0.9-15

IRanges2.42.0

irGSEA3.3.2

irlba2.3.5.1

iSC.MEB1.0

isoband0.2.7

iterators1.0.14

iterpc0.4.2

janeaustenr1.0.0

JASPAR20200.99.10

jjAnno0.0.3

jjPlot0.0.3

jomo2.7-6

jpeg0.1-11

jquerylib0.1.4

jsonlite2.0.0

jsonvalidate1.5.0

juicyjuice0.1.0

KEGGREST1.48.1

Kendall2.2.1

keras2.15.0

kernlab0.9-33

KernSmooth2.23-26

khroma1.16.0

knitr1.50

ks1.15.1

kuenm1.1.10

labeling0.4.3

lambda.r1.2.4

later1.4.2

lattice0.22-7

latticeExtra0.6-30

lava1.8.1

lazyeval0.2.2

leaps3.2

leidenbase0.1.35

lhs1.2.0

libcoin1.0-10

lifecycle1.0.4

lime0.5.3

limma3.64.3

linprog0.9-4

listenv0.9.1

litedown0.7

lme41.1-37

lmom3.2

Lmoments1.3-1

lmtest0.9-40

locfit1.5-9.12

lpSolve5.6.23

lubridate1.9.4

magic1.6-1

magick2.8.7

magrittr2.0.3

maps3.4.3

markdown2.0

MASS7.3-65

MAST1.33.0

Matrix1.7-3

MatrixGenerics1.20.0

MatrixModels0.5-4

matrixStats1.5.0

maxnet0.1.4

maxstat0.7-26

mclust6.1.1

mcmc0.9-8

MCMCpack1.7-1

memoise2.0.1

memuse4.2-3

MendelianRandomization0.10.0

metabolomicsR1.1.0

METAFlux0.0.0.9000

metapod1.16.0

methods4.5.1

Metrics0.1.4

mets1.3.7

Mfuzz2.68.0

mgcv1.9-3

mice3.18.0

microbenchmark1.5.0

mime0.13

miniUI0.1.2

minqa1.2.8

mitml0.4-5

mixsqp0.3-54

mixtools2.0.0.1

mlr2.19.2

mlrMBO1.1.5.1

MMAPPR20.99.22

ModelMetrics1.2.2.2

modelr0.1.11

modeltools0.2-24

monocle2.36.0

monocle31.3.7

moonBook0.3.1

mr.raps0.4.2

MRMix0.1.0

MRPRESSO1.0

msigdbr25.1.1

multcomp1.4-28

multcompView0.1-10

multicool1.0.1

multimode1.5

MungeSumstats1.16.0

munsell0.5.1

mvtnorm1.3-3

mycor0.1.1

N2R1.0.3

naivebayes1.0.0

ncdf41.24

Nebulosa1.18.0

network1.19.0

nichenetr2.2.0

nlme3.1-168

nloptr2.2.1

NLP0.3-2

NMF0.28

nnet7.3-20

nnls1.6

nortest1.0-4

numDeriv2016.8-1.1

officer0.7.0

openalexR2.0.1

openssl2.3.3

openxlsx4.2.8

optparse1.7.5

ordinal2023.12-4.1

org.Hs.eg.db3.21.0

org.Mm.eg.db3.21.0

osqp0.6.3.3

pagoda21.0.12

pak0.9.0

paletteer1.6.0

pammtools0.7.3

pan1.9

parallel4.5.1

parallelDist0.2.6

ParallelLogger3.4.2

parallelly1.45.1

parallelMap1.5.1

ParamHelpers1.14.2

patchwork1.3.1

pbapply1.7-4

pbkrtest0.5.5

pbmcapply1.5.1

pcaMethods2.0.0

pcaPP2.0-5

pec2025.06.24

pheatmap1.0.13

phyclust0.1-34

pillar1.11.0

pkgbuild1.4.8

pkgconfig2.0.3

pkgdown2.1.3

pkgload1.4.0

plinkbinr0.0.0.9000

plogr0.2.0

plotly4.11.0

plotrix3.8-4

plotROC2.3.3

plyr1.8.9

png0.1-8

polspline1.1.25

Polychrome1.5.4

polyclip1.10-7

polynom1.4-1

poweRlaw1.0.0

ppcor1.1

pracma2.4.4

praise1.0.0

preprocessCore1.70.0

PresenceAbsence1.1.11

presto1.0.0

prettyunits1.2.0

princurve2.1.6

prismatic1.1.2

pROC1.19.0.1

processx3.8.6

prodlim2025.04.28

profvis0.4.0

progeny1.30.0

progress1.2.3

progressr0.15.1

promises1.3.3

ProtGenerics1.40.0

proxy0.4-27

proxyC0.5.2

ps1.9.1

pscl1.5.9

Publish2025.07.24

pubmedR0.0.3

purrr1.1.0

pwalign1.4.0

qlcMatrix0.9.9

qs0.27.3

quantreg6.1

qvalue2.40.0

R.cache0.17.0

R.methodsS31.8.2

R.oo1.27.1

R.utils2.13.0

R62.6.1

RadialMR1.2

ragg1.4.0

randomForest4.7-1.2

randomForestSRC3.4.1

ranger0.17.0

RANN2.6.2

RApiSerialize0.1.4

rappdirs0.3.3

raster3.6-32

RBGL1.84.0

rbibutils2.3

RcisTarget1.28.1

rcmdcheck1.4.0

RColorBrewer1.1-3

Rcpp1.1.0

RcppAnnoy0.0.22

RcppArmadillo14.6.0-1

RcppEigen0.3.4.0.2

RcppHNSW0.6.0

RcppML0.3.7

RcppParallel5.1.10

RcppProgress0.4.2

RcppRoll0.3.1

RcppSpdlog0.0.22

RcppTOML0.2.3

RcppZiggurat0.1.8

RCurl1.98-1.17

Rdpack2.6.4

reactable0.4.4

reactR0.6.1

readr2.1.5

readxl1.4.5

recipes1.3.1

reformulas0.4.1

registry0.5-1

rematch2.0.0

rematch22.1.2

remotes2.5.0

rentrez1.2.4

reprex2.1.1

reshape0.8.10

reshape21.4.4

ResidualMatrix1.18.0

restfulr0.0.16

reticulate1.43.0

Rfast2.1.5.1

Rfast20.1.5.4

rhdf52.52.1

rhdf5filters1.20.0

Rhdf5lib1.30.0

RhpcBLASctl0.23-42

Rhtslib3.4.0

Rigraphlib1.0.0

riskRegression2025.05.20

rjags4-17

rJava1.0-11

rjson0.2.23

rlang1.1.6

rlist0.4.6.2

rly1.7.4

rmarkdown2.29

rms8.0-0

RMTstat0.3.1

Rnanoflann0.0.3

rngtools1.5.2

robustbase0.99-4-1

RobustRankAggreg1.2.1

ROCR1.0-11

ROI1.0-1

Rook1.2

rootSolve1.8.2.4

roxygen27.3.2

rpart4.1.24

rprojroot2.1.0

rrcov1.7-7

rsample1.3.1

Rsamtools2.24.0

rscopus0.9.0

rsnps0.6.1

RSpectra0.16-2

RSQLite2.4.2

rstatix0.7.2

rstudioapi0.17.1

rsvd1.0.5

rtracklayer1.66.0

Rtsne0.17

RUnit0.4.33.1

rvcheck0.2.1

rversions2.1.2

rvest1.0.4

s21.1.9

S4Arrays1.8.1

S4Vectors0.48.1

S70.2.0

safetensors0.2.0

sandwich3.1-1

sass0.4.10

SC31.36.0

scAB1.0.0

ScaledMatrix1.16.0

scales1.4.0

scam1.2-19

scater1.36.0

scattermore1.2

scatterpie0.2.5

scatterplot3d0.3-44

sccore1.0.6

scde2.36.0

SCENIC1.3.1

scHCL0.1.1

scico1.5.0

scID2.2

SCINA1.2.0

Scissor2.0.0

scmap1.30.0

SCopeLoomR0.13.0

SCP0.5.6

SCpubr2.0.2

scran1.36.0

scrapper1.2.1

scRNAtoolVis0.1.0

scTenifoldKnk1.0.3

scTenifoldNet1.3

sctransform0.4.2

scuttle1.18.0

segmented2.1-4

selectr0.4-2

Seqinfo1.0.0

seqLogo1.74.0

sessioninfo1.2.3

Seurat5.3.0

SeuratData0.2.2.9002

SeuratObject5.1.0

SeuratWrappers0.4.0

sf1.0-21

sfsmisc1.1-21

sgeostat1.0-27

shadowtext0.1.5

shape1.4.6.1

shiny1.11.1

shinyBS0.61.1

shinycssloaders1.1.0

shinydashboard0.7.3

shinyFiles0.9.3

shinyjs2.1.0

shinythemes1.2.0

shinyWidgets0.9.0

ShortRead1.66.0

Signac1.14.9002

simona1.6.0

simplifyEnrichment2.2.0

SingleCellExperiment1.30.1

singleCellNet0.1.0

SingleR2.10.0

singscore1.28.0

sitmo2.0.2

sjlabelled1.2.0

sjmisc2.8.11

slam0.1-55

slider0.3.2

slingshot2.16.0

smoof1.6.0.3

sna2.8

snow0.4-4

SnowballC0.7.1

snowfall1.84-6.3

softImpute1.4-3

sourcetools0.1.7-1

sp2.2-0

spacetime1.3-3

spam2.11-1

spaMM4.6.1

SparseArray1.8.1

SparseM1.84-2

sparseMatrixStats1.20.0

sparsesvd0.2-2

sparsevctrs0.3.4

spatial7.3-18

SpatialCPie1.24.0

SpatialDDLS1.0.3

SpatialExperiment1.18.1

spatialLIBD1.20.1

spatstat.data3.1-6

spatstat.explore3.5-2

spatstat.geom3.5-0

spatstat.random3.4-1

spatstat.sparse3.1-0

spatstat.univar3.1-4

spatstat.utils3.1-5

spData2.3.4

spdep1.3-13

speedglm0.3-5

splancs2.01-45

splines4.5.1

SQUAREM2021.1

statmod1.5.0

statnet.common4.12.0

stats4.5.1

stats44.5.1

stringdist0.9.15

stringfish0.17.0

stringi1.8.7

stringr1.5.1

SummarizedExperiment1.38.1

survival3.8-3

survminer0.5.2

susieR0.14.2

sva3.56.0

svglite2.2.1

svMisc1.4.3

sys3.4.3

systemfonts1.2.3

tcltk4.5.1

TCseq1.32.0

tensor1.5.1

tensorflow2.16.0

terra1.8-60

tester0.2.0

testthat3.2.3

textshaping1.0.1

tfautograph0.3.2

TFBSTools1.46.0

TFMPvalue0.0.9

tfruns1.5.3

TH.data1.1-3

tibble3.3.0

tidycmprsk1.1.0

tidygraph1.3.1

tidyr1.3.1

tidyselect1.2.1

tidytext0.4.3

tidytree0.4.6

tidyverse2.0.0

tiff0.1-12

timechange0.3.0

timeDate4041.110

timereg2.0.7

tinytex0.57

tkWidgets1.86.0

tm0.7-16

tokenizers0.3.0

tools4.5.1

torch0.16.0

TrajectoryUtils1.16.1

treeio1.32.0

triebeard0.4.1

tweenr2.0.3

TwoSampleMR0.6.14

txdbmaker1.4.2

tzdb0.5.0

UCell2.12.0

ucminf1.2.2

UCSC.utils1.4.0

umap0.2.10.0

units0.8-7

urlchecker1.0.1

urltools1.7.3.1

usethis3.1.0

utf81.2.6

utils4.5.1

uuid1.2-1

uwot0.2.3

V86.0.5

VariantAnnotation1.54.1

VariantTools1.50.0

vctrs0.6.5

velocyto.R0.6

VennDiagram1.7.3

VGAM1.1-13

viper1.42.0

vipor0.4.7

viridis0.6.5

viridisLite0.4.2

visNetwork2.1.2

vroom1.6.5

waiter0.2.5

waldo0.6.2

warp0.2.1

WGCNA1.73

whisker0.4.1

widgetTools1.86.0

withr3.0.2

wk0.9.4

wordspace0.2-8

writexl1.5.4

WriteXLS6.8.0

wrMisc1.15.4

xfun0.52

XML3.99-0.18

xml21.3.8

xopen1.0.1

xtable1.8-4

xts0.14.1

XVector0.48.0

yaImpute1.0-34.1

yaml2.3.10

yulab.utils0.2.0

zeallot0.2.0

zigg0.0.2

zinbwave1.30.0

zip2.3.3

zlibbioc1.54.0

zoo1.8-14