future_plugins.txt

Note: Some of these may be server-based

SHAMAN
AlienTrimmer
Pear

Seurat

MM_GBSA
NN_Rosetta

Pangenome software->
Roary (tries to read from nonexistent intermediate folders, have never been able to resolve this problem)
GET_HOMOLOGUES, need to take time to learn R features
ITEP, can't find
PanOCT, missing Perl dependencies
PGAP, missing CWL facilities
PanViz, uses Javascript
EUPAN, did not compile
Panseq, missing Perl dependencies
PanGet, missing Perl dependencies
micropan, need to take time to learn R features
DeNoGAP, missing Perl dependencies
PanACEA, error while running
PanCake, multiple dependent commands, missing some steps
Panaconda, requires Python 2, last update 2017
PanConFun, can't find
Piggy, requires Roary, which doesn't currently work
seq-seq-pan, requires snakemake, no standard installation available
NGSPanPipe, another workflow with multiple commands, need time to learn



MGMapper
ORCA
BioBoxes
Biocontainers
Scoary
Islandviewer
EGID
PredictBias

Genomic/DNA-based
ABSOLUTE
EXPANDS
MATH
PhyloWGS

Transcriptomic
tITH
sITH
DEPTH

Seaborn (scatter plots)


Compound Discoverer 3.1
MS-DIAL
CSI:FingerID
CFM-ID
MS-FINDER
MetFrag
MS2LDA
Metaboanalyst
FELLA (R package)
ChemRICH
MetaMapp
Pathview
Metscape

 MANIEA (when released)
 MENA pipeline (MENAP)
 https://cran.r-project.org/web/packages/pcalg/index.html  (Causality algorithms)
+
+Covid-19 Pipeline
+SWISS-MODEL
+PatchDock
+HADDOCK
+FireDock
+Vaxjen
+AlgPred
+SOLpro
+Expasy Protparam
+RAMPAGE (Ramachandran)


RAMMCAP
MetaVelvet
SOAPdenovo2
MOCAT
SmashCommunity
FANTOM
MetaCV
Phymm

DUST
ALLPATH
ESOM
CLAMS
Amplicon Noise
CRT
PILER-CR
SILVANGS

(Have links for these)
Genomemeta
SOrt-ITEMS
DiScRiBinATE
MetaVelvet
RayMeta
MetaGeneMark
GlimmerMG
BLASTX
MetaORFA
MinPath
MetaPath
GhostKOALA
ProVIDE
Metagenome Seq
Shotgun Functionalize (R)
IMG/M
Phinch
CAMERA
Meta Comp

DCA
Zachs Algorithms
VAST
diSBPred
DALI
SSAP
SWORD
SWIPE
Prokka+friends
MUMmer

SABRE
idemp
fastx_toolkit
Breakaway
trimmomatic
bbtols
SEPP
TIPP

MaAsLin2 

Maaft

Flint
Jasper
AMBER

Machine Learning
BERT
* CAE (Concrete Autoencoder) (ERRORS)
DEG
Logistic Regression
VAE (ERRORS)
GAN
KNN (K-Nearest Neighbor)
DT
CRF

FATCAT
ProtoMol

Docker/CUDA
https://github.com/NVIDIA/nvidia-docker

TPMCalculator
CAPE
SNPDel

MEME-MAST
eMOMs (Vitalii GitHub) 
RANSAC 
Masif
Chainer
MXNet
PyTorch
Reverse Complement
PALM (Pipeline for Analysis of Longitudinal Multi-Omics Data)
Reverse Best Blast
Enrichment (Giri)
ConSurf
Masif
Tigramite
PyCausal

(Evolution)
MCI
SGS
IG
GES
tsGFCI

(Bayesian Networks)
BN
DBN
CGDBN
2TDBN

See (giriemail)
SOM
Monocle2
GTMLLE
Sammon
Splatter Paths
Isomap
viSNE

Orthovenn [Current Bug: Hanging]

Pipelines
Bubble Chart
Overlap Tests (DB and SW)

RFE
RF
Survival Analysis

CLC Genomics
SMRT Portal

Rust-Bio functions (cf. Koster et al, 2015)
Rosalind Bioinformatics Collection

16S datasets - MicrobiomeHD Database
16S processing pipeline (Duvallet et al, 2017): https://github.com/thomasgurry/amplicon_sequencing_pipeline
R machine learning
https://en.wikipedia.org/wiki/List_of_RNA-Seq_bioinformatics_tools

NirvanaBiome -> Autism and WGS
MANIEA (when released)
MENA pipeline (MENAP)
https://cran.r-project.org/web/packages/pcalg/index.html  (Causality algorithms)

RFE (Recursive Feature Elimination)
GGTREE
JALVIEW
YULAB-SMU.TOP/TREEDATA-BOOK/

ShortBRED
M2mini2
cms+
IEomics
LipidQC
LipdMatch
LipdPrimer
Vitalli MM pipeline
FLIPPER
PRINSEQ -> Cannot install, dated version of Cairo
MEtaxa2
CARD
RGPs
PanSeq
AGEnt
SIGI-HMM
PAI-IDA
Centroid
PredictBas
MobileFinder