Package: PSSMCOOL 0.2.2

Alireza mohammadi

PSSMCOOL: Features Extracted from Position Specific Scoring Matrix (PSSM)

Returns almost all features that has been extracted from Position Specific Scoring Matrix (PSSM) so far, which is a matrix of L rows (L is protein length) and 20 columns produced by 'PSI-BLAST' which is a program to produce PSSM Matrix from multiple sequence alignment of proteins see <https://www.ncbi.nlm.nih.gov/books/NBK2590/> for mor details. some of these features are described in Zahiri, J., et al.(2013) <doi:10.1016/j.ygeno.2013.05.006>, Saini, H., et al.(2016) <doi:10.17706/jsw.11.8.756-767>, Ding, S., et al.(2014) <doi:10.1016/j.biochi.2013.09.013>, Cheng, C.W., et al.(2008) <doi:10.1186/1471-2105-9-S12-S6>, Juan, E.Y., et al.(2009) <doi:10.1109/CISIS.2009.194>.

Authors:Javad zahiri [aut], Alireza mohammadi [aut, cre]

# Install 'PSSMCOOL' in R:

install.packages('PSSMCOOL', repos = c('https://biocool-lab.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Last updated from:65e1c4e91c. Checks:7 WARNING, 1 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	WARNING	170
source / vignettes	ERROR	352
linux-release-x86_64	WARNING	127
macos-release-arm64	WARNING	196
macos-oldrel-arm64	WARNING	163
windows-devel	WARNING	114
windows-release	WARNING	147
windows-oldrel	WARNING	108
wasm-release	OK	118

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
PSSMCOOL:Extracting Various Feature vectors from PSSM Matrix	PSSMCOOL-package
AATP_TPC feature vector	AATP_TPCC
AB-PSSM and RPM-PSSM feature vector	AB_PSSM
Averag Block feature vector	Averag_Block
consunsus_sequence	consunsus_sequence
CSP-SegPseP-SegACP feature vector	CS_PSe_PSSM
DMACA-PSSM feature	DFMCA_PSSM
Discrete Cosin Transform Feature	Discrete_Cosine_Transform
Disulfide connectivity feature	disulfid
DP_PSSM feature vector	DP_PSSM
DPC-PSSM,AAC-PSSM and AADP-PSSM feature vectors	DPC_PSSM
discrete wavelet transform feature vector	dwt_PSSM
EDP_EEDP_MEDP feature vector	EDP_MEDP
D-FPSSM and SF-PSSM feature vectors	FPSSM
Mixture of Two FPSSM Features	FPSSM2
grey pssm feature vector	grey_pssm_pseAAC
3-mer and 2-mer in dataframe	k_mers
k_seperated_bigrame feature vector	k_seperated_bigrame
kiderafactor feature	kiderafactor
Linear predictive coding feature	LPC_PSSM
MBMGACPSSM feature	MBMGACPSSM
pseudo position-specific scoring matrix feature	pse_pssm
auto covariance transformation feature vector	pssm_ac
Cross covarianse feature vector	pssm_cc
PSSM-SD feature	PSSM_SD
PSSM-Seg feature vector	pssm_seg
PSSM400 feature	pssm400
PSSMAC feature	PSSMAC
PSSM BLOCK feature vector	PSSMBLOCK
RPSSM feature	rpssm
SCSH Feature vector	scsh2
single Average feature	single_Average
smoothed PSSM feature	smoothed_PSSM
SOMA PSSM Feature	SOMA_PSSM
Singular Value Decomposition (SVD)	SVD_PSSM
3-Mer and 2-Mer	three_mer
trigrame feature vector	trigrame_pssm