I have a list of accession numbers about 5000plus. I want to pull down the protein names for this list of ids, I have.
Can someone guide how can I do it using R programming ?
Dear Alok Patra
These links might be helpful, have a look:
1. https://cran.r-project.org/web/packages/UniprotR/UniprotR.pdf
2. https://www.biostars.org/p/432321/
3. https://www.ncbi.nlm.nih.gov/guide/howto/dwn-records/
Kind Regards
Qamar Ul Islam
As mentioned by Qamar Ul Islam , I suggest using the UniprotR package and its function GetNamesTaxa().
Best wishes,
Francesco
Try Biomartr
# Install core Bioconductor packages if (!requireNamespace("BiocManager")) install.packages("BiocManager") BiocManager::install()
# Install package dependencies BiocManager::install("Biostrings", version = "3.8") BiocManager::install("biomaRt", version = "3.8")
# install biomartr 0.9.0 install.packages("biomartr", dependencies = TRUE)
#example 1 from NCBI
HS.proteome.genbank
Dear Francesco Sanmarchi
Thank you for your appreciation and recommendation.
Stay Happy Stay Healthy.
Thank you all for the suggestions. Appreciate your timely help.
I managed to use, BiomaRt, Bioconductor R package.
Reference link:
https://m.ensembl.org/info/data/biomart/biomart_r_package.html
Instead of checking only the mRNA level, I want to check the active protein level of MMP-1 in Liver tissue from mice. How can I do that?
03 March 2021 1,763 2 View
I want to analyses the proportion of swimming sperm of three species of fish in two salinities. To analyse the proportion of swimming sperm in a Generalized Linear Model, I would use a Binary...
03 March 2021 2,297 3 View
03 March 2021 8,272 1 View
Hi. Please tell me what guidelines should i need to follow for questionaries' type research work in India. It is not hospital based work, we are conduction basic institutional based qualitative...
03 March 2021 2,037 3 View
Hi, I implemented a code to gabor filter cifar10 data but the images after being filtered and stacked are not clear like the original images. I think the problem is in the way I am using the...
03 March 2021 6,317 1 View
i am try to classify the x-ray images. During classification , can i block unwanted images (except x-ray image).
03 March 2021 7,100 1 View
03 March 2021 5,360 2 View
The term miscibility refers to the single-phase state in thermodynamics. I do not mean the compatibility of different components. To determine the miscibility I know several techniques such as...
03 March 2021 4,107 4 View
If the detection range is in ng/ml but the reference range is in ug/ml for a molecule or protein in serum or plasma .how to dilute and what is the initial volume to be taken for quantitative analysis
02 March 2021 7,670 3 View
02 March 2021 5,204 3 View
Good afternoon, I recently used OmniLog from BIOLOG for my experimentations : I tested the metabolism of different strains on 2 types of plates. I have 16 strains of 3 different groups...
02 March 2021 3,584 1 View
Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...
02 March 2021 4,569 4 View
Which is suitable for use with Python? MySQL or SQL Server? What is your suggestion?
01 March 2021 3,422 3 View
I wanted to add an extra parameter to the existing Johnson cook equation in the ABAQUS simulation. How to add those extra parameters. Ref: A modified Johnson-Cook material model with strain...
28 February 2021 4,841 3 View
In R-studio, there are many commands of Gumbel package. Arguments are also different. I`m asking about the alpha parameter of the Copula which must be greater than 1. If this is the one used to...
25 February 2021 5,229 3 View
I understand there are a lot of software programs that can simulate DED by going through specific modeling, simulation, and commands. For me, that was time consuming and results were not accurate....
24 February 2021 4,428 3 View
Hello everyone: I am looking for a simple software program to model chemical bonds. The purpose is to generate a high-quality graphical abstract for a top leading journal in the field of...
23 February 2021 8,012 3 View
I am looking for implementation of bayesian decision trees and bayesian regression trees in Python and/or R.. Do you know if the existing libraries support this
23 February 2021 6,689 3 View
To be specific, I want to conduct an IV regression in stata with the following three equations. EQ1: Y1 ~Y2 Y3 X EQ2: Y2 ~ Z1 EQ3: Y3 ~ Z2 Both Y2 and Y3 are endogenous. However, Z1 and Z2 are...
23 February 2021 6,266 3 View
My real system (buck converter) can only take an input of 0 to 1 (duty ratio) and I need to constrain the system so the controller action keeps within this bounds. How can I do this? The code for...
22 February 2021 2,125 3 View