How to open SOFT file for GEO database?

More Greeshma Thulasi's questions See All

How to extract each exon into separate file from a multifasta file?

I have a multifasta file containing gene sequence of HLA A gene. I want to extract each exon into separate fasta file. Example of data file is attached: >HLA:HLA00001 A*01:01:01:01 1098...

26 April 2023 7,748 3 View

Are there any online database depository for actigraphy performed in children (day and/or nocturnal)?

I'm looking for online database depository (possible for collaboration too) of actigraphy activities performed on the children and young adolescents during daytime (in school, house or any...

23 November 2022 1,493 0 View

How to construct the input for multi-structural material in quantum espresso ?

The material I'm working has been found in a mixed state of different space groups experimentally. My question is that 1. Can such multi-structural calculation be done in quantum espresso ? 2. If...

19 November 2022 9,112 3 View

What is the reason for getting low cfDNA concentration in blood serum, while using Qiagen kit?

We are using QIAamp DNA mini kit(250) to extract cfDNA from whole blood. While checking DNA concentration in Qubit, continuously getting ' low concentration ' (TOO LOW) for multiple...

27 October 2020 6,973 3 View

How to recover frozen LUHMES cells without contamination?

HI, I am trying to recover frozen LUHMES cells bought from commercial source and encountered bacterial contamination twice on the 2nd day after thawing. I am confident that the contamination is...

12 August 2019 7,264 1 View

Why people prefer open Seasame over psychtoolbox?

I am keen interested to know advantages of open Sesame over psychtoolbox. And what would researcher prefer when designing ERP paradigm: open Seasame or psychtoolbox?

23 March 2019 9,312 4 View

Where can I get authenticate datasets of fMRI, EEG, ECG,and Eye tracking data?

I would like to know source of data-sets where I can download data easily without any obstacle.

08 June 2018 2,287 5 View

What if the standard that I use for generating standard curve for Absolute quantification of qPCR doesn't express my gene of interest?

I am working on neural differentiation of dental pulp stem cells (DPSC). I am checking some ion channels that play role in the differentiation and want to do an absolute quantification of my qPCR...

11 February 2018 1,891 3 View

What are the differences in EEG brain rhythms when eye is closed and when eye is opened?

Can we tell differences by looking at EEG signal that person has open eye or close eye?

05 December 2017 7,443 3 View

Anyone has experienced Metal corrosion on Miseq Flow Cell stage?

We have been observing white salt deposits over the flow cell stage for quite some time. And now that we have concluded that it is no longer salt deposits, its the corroded metal. Is there anybody...

01 November 2016 3,905 3 View

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

Seeking Software Recommendations for SELEX NGS Data Analysis?

I am looking for software to help analyze SELEX NGS data, including alignment, sequence enrichment, and other related tasks. Can anyone recommend suitable tools or software? Best wishes, Waleed

30 July 2024 1,061 5 View

CAD File of human's & rat's respiratory airways ?

Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...

29 July 2024 1,092 2 View

Could you try using PeptiCloud and see if it's a useful tool for biology research?

PeptiCloud (www.pepticloud.com) is a bioinformatic platform that allows researchers to organize and share their data for their projects as well as collaborate with others in one place. Through...

28 July 2024 4,762 2 View

Should the amount of DNA input used for ChIP-seq library preparation be matched between the control and experimental groups?

Hi all. As a beginner in ChIP-seq experiments, I hope you understand that the following questions might be somewhat basic. I am planning to perform ChIP-seq or MeDIP-seq analysis to investigate...

28 July 2024 6,938 1 View

MDCI module in Orca software?

Dear Researchers, My question is associated with the "MDCI" method in Orca. Please let me clarify my question using a simple example: Suppose we are going to perform CBS extrapolation using "!...

21 July 2024 1,632 0 View

How to use NCBI datasets ?

I have been trying to extract genome from NCBI using their dataset tool, however some examples seem not to work : ./datasets download genome taxon "Homo Sapiens" --annotated --assembly-level...

20 July 2024 1,339 2 View

What is wrong with my input file?

im studing gaussian 16 with reading paper about I-131 Metaiodobenzylguanidine in the paper "In a similar vein, nuclear magnetic resonance shielding values were investigated using the widely...

16 July 2024 6,040 4 View

Printing residues in an object in Pymol?

Hi! I am currently working on a protein where I have selected residues within 10A of its bound ligand in pymol. However, I can not find a way to print out what residues are contained in that group...

15 July 2024 1,727 1 View

I came across oscillations in a pressure profile for a pipeline flow along the axis of a cylinder, how do I prove that these are not numerical err?

In terms of CFD, we often analyze the stability of the error using Von-Neumann analysis, especially for FDM based problems. Should we follow the same approach for a compressible fluid flow using FVM ?

13 July 2024 6,296 5 View

Pranavathiyani G Popular answer

You can use R/Bio-conductor for other format conversions and also for micro-array data analysis. Check out the following links.

http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/geo/

https://mdozmorov.github.io/BIOS567/assets/presentation_Bioconductor/GEO.pdf

https://www.bioconductor.org/packages/devel/bioc/vignettes/GEOquery/inst/doc/GEOquery.html

http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor/

Pranavathiyani G