5
votes
Accepted
Retrieve abstract/summary for NCBI bookshelf via Entrez
Entrez requires the unique identifiers(UID) for fetching related info. The id you are using in the query is RID. I guess that why you are getting ...
- 604
4
votes
How to access organism IDS, taxon nodes from UniProt?
These are NCBI taxonomy ID's rather than anything specific to UniProt. One way to parse them would be using BioPython via Bio.Entrez, for example:
...
- 3,968
4
votes
How to interconvert InChI and InChIKey?
Recently I've developed a python lib for converting InChI to InChIKey: https://github.com/liwt31/chembl_ikey. Maybe it will help.
- 141
4
votes
Automating sequence download from Wormbase
Further inspecting the source code of the downloaded page, I found the following:
...
- 3,205
4
votes
Accepted
List of human transcription factors
Lambert et al. (2018, Cell. 172(4):650-665) provide a manually curated list of human TFs at this website.
- 2,644
4
votes
Where can I find examples of published bioinformatics pipeline packages?
The GATK team maintains a GitHub repository with their pipelines: https://github.com/gatk-workflows. They use the Cromwell Workflow Management System, an open source tool created by the Broad ...
- 10.6k
4
votes
Where can I find examples of published bioinformatics pipeline packages?
I think the nextflow core (https://nf-co.re) pipelines should satisfy most of your requirements. These pipelines are written in nextflow (https://nextflow.io) which allows scaling from personal to hpc ...
- 136
3
votes
Accepted
3
votes
Accepted
NCBI retrieve genome assembly with splicing or "modifications"
The page you link to is a GenBank Flat file, the default format used by GenBank. So, to get that format, which includes the join lines, use:
...
- 10.6k
3
votes
Accepted
Where to download baseline/average gene expression level of all human coding genes?
There is not going to be a public database with this data. Apart from anything else, generating data for early human development is difficult and ethically tricky. Also, most people who care about ...
- 3,341
3
votes
Retrieve abstract/summary for NCBI bookshelf via Entrez
As arupgsh says, you need to use esearch to get a list of unique identifiers before using efetch to retrieve info about each result. I think the easiest way to do this is to use Entrez Direct, which ...
- 1,816
2
votes
Accepted
How to retrieve InChI key for KEGG compound?
I'm not aware of a functionality in the KEGG service that would allow you to do that directly. I believe your solution (using e.g. ChEBI) is the correct one.
You may have other useful service such ...
- 36
2
votes
Accepted
CRISPR Sequence Finder and Database Download
CRT (CRISPR Recognition Tool) http://www.room220.com/crt/
Crisprs Finder Online Tool https://crispr.i2bc.paris-saclay.fr/Server/
Piler-CR http://www.drive5.com/pilercr/
(Omic Tools List) https://...
- 173
2
votes
Accepted
Retrieving Metabolic networks from WIT Database
It seems like there are some files related to the databases at the ftp site: http://ftp.mcs.anl.gov/pub/WIT2/. The related files were last updated on 2002.
I found it via searching at google: ...
- 4,721
2
votes
How can I obtain FTP links to studies in ENA given a BioProject ID?
Here are some command lines I used for that purpose in bash.
Simply prepare a text file containing each accession number (SRR/ERR) you want and create a for loop. Here I used prozilla to speed up ...
2
votes
Accepted
Are there databases or resources that contain expression of proteins or genes before and after cancer treatment?
One such database/tool is “[PharmacoGx][1]: an R package for analysis of large pharmacogenomic datasets.” Bioinformatics (Oxford, England).
They brought together a ...
- 4,202
2
votes
1
vote
Accepted
Finding related Mesh Terms given a substance
Your question encompasses a number of different scenarios:
Your search term is not the primary label for the MeSH concept, but is an accepted alias or synonym (which may or may not be recorded in ...
- 274
1
vote
I have few genes and would like to retrieve their gene expression. Please any one help me how to retrieve the gene expression
For a few genes you may just explore them in ENSEMBL, ENSEMBL AKT1
- 398
1
vote
Accepted
Print specific columns in a matrix on the basis of sample id's in the header
Example in R. If you have a file of column names, names.txt, such as:
mpg
cyl
disp
and a data.frame like ...
- 1,789
1
vote
Print specific columns in a matrix on the basis of sample id's in the header
There's a million different ways to do simple taks like this. Pick one and learn it:) Python is my go to as it can do pretty much everything you'd ever want. I saved your example as csv with no spaces ...
- 579
1
vote
How can I obtain FTP links to studies in ENA given a BioProject ID?
They have an API you can interact with.
If you need to get files for only a few different projects:
Search for your accession ID in the browser (leading to https://www.ebi.ac.uk/ena/browser/view/...
- 716
1
vote
GDC data portal cancer subtype
These data are in Experiment Hub in Bioconductor
library(curatedTCGAData)
brcaRNA <- curatedTCGAData("BRCA", "RNASeq2GeneNorm", dry.run = FALSE)
- 156
1
vote
GDC data portal cancer subtype
I personally find the GDC portal not very user-friendly. However, some of the data is available from other sources. For example, you can download TCGA-BRCA FPKMs and phenotypes from UCSC Xena here: ...
- 2,209
1
vote
Blueprint replicates
Blueprint does not have technical replicates, you will find that very few sequencing based experiments ever have technical replicates. As biological replicates: each individual is regarded as a ...
- 3,341
1
vote
NCBI - edirect suite to download all genome sequences associated with a query - troubleshooting
If you want to find version info you can either :
Ask for another edirect tool version (it will be the same version for edirect) :
efetch -version
6.80
Check ...
- 41
1
vote
Accepted
NCBI - edirect suite to download all genome sequences associated with a query - troubleshooting
The issue here was I was using an older version of eDirect. There is no command to check version or updates. Your best bet is if you experience problems uninstall and reinstall.
- 965
1
vote
Accepted
How to access organism IDS, taxon nodes from UniProt?
That file is actually trivial to parse. You only care about lines that have N=$species, so you can simply do:
...
- 10.6k
1
vote
How to interconvert InChI and InChIKey?
Not sure if directly possible in bioservices but one can do the following workaround using chemspider:
...
- 743
1
vote
How to retrieve logical expressions (KO based) for reactions from KEGG?
Some information seems to be available on the module level utilising the API.
Reaction R00352 points to the module M00173. While some information is in the ...
- 261
Only top scored, non community-wiki answers of a minimum length are eligible