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- 3PCLR
- 3d-dna
- 4p
- AAFTF
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- ABySS
- ACLs
- ACTC
- ADFRsuite
- ADMB
- ADMIXTURE
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- AI Education and Training
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- AI reference dataset hosting policy
- ALFA
- ALLMAPS
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- Amrfinderplus
- Ancestryhmm
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- Annotated SLURM Script
- Ansible
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- Bam-Readcount
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- Basic Linux Use
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- Bayenv
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- BayesR
- BayesTraits
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- Bcftools
- Bcl2fastq
- Bertini
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- Bifrost
- Bigslice
- BinPacker
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- Biolite
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- Blast2GO
- Blast2GO CLI
- Blender
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- BlobTools
- Blocked Accounts
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- Bsmap
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- Bxh xcede tools
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- CMS
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- DVGfinder
- Dadi
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- Dancemapper
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- Datamash
- Dcmstack
- DeFusion
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- DealII
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- DeepARG
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- DeepLabCut
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- Deepvariant
- Delft3D Configuration
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- Delly
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- Desmond
- Detectron2
- DiCal2
- Diamond
- DiffReps
- Disbatch
- DiscoVista
- Discvrseq
- Distruct
- Dlib
- DoGFinder
- Dorado
- DosageConvertor
- Doxygen
- Dragmap
- Dragonflye
- Dram
- Dretools
- Dropseq
- Dsistudio
- Dtiprep
- Duchamp
- DynamicDBG
- Dynare
- Dynasor
- EAGLE
- ECE
- EDTA
- EDirect
- EEGLAB
- EGSnrc
- EGene-MVN
- EIGENSOFT
- ELPA
- EMAN2
- EMC
- EMMAX
- EPACTS
- EQTLA
- EQtlBma
- ESOM
- ESPRIT
- ETE3
- EVidenceModeler
- EXpress
- Ea-utils
- Eagle-rc
- Eddy-squeeze
- Edyeet
- EggNOG-mapper
- ElPrep
- Elastix
- Emacs
- Email storage alert
- Embree
- Emerald
- EnTAP
- EnergyPlus
- Ensembl Tools
- EpiNano
- Epiteome
- Epoch
- Erpin
- Esmf
- Eukulele
- Evigene
- EvoLSTM
- ExaBayes
- Exonerate
- ExpansionHunter
- ExpansionHunterDenovo
- Export2graphlan
- Ezaai
- FALCON unzip
- FAR
- FAST
- FASTA
- FASTRAL-constrained
- FASTphase
- FDSTools
- FEELnc
- FEniCS
- FFTW