Question: spreadsheet tools alternative
1
gravatar for sacha
2.9 years ago by
sacha1.9k
France
sacha1.9k wrote:

Hi,

As you know, Excel is not safe to do bioinformatics stuff because it changes your data. https://www.ncbi.nlm.nih.gov/pubmed/15214961.
I guess biologist can disable those features, but it seems to hard.

Do you know other simple spreadsheet software which can be used by biologist ? Something like : TSV/CSV editor ?

gui spreadsheet excel • 1.2k views
ADD COMMENTlink modified 2.9 years ago by Alex Reynolds30k • written 2.9 years ago by sacha1.9k
1

This is not a fair question. You are saying it's too hard to adjust some settings in Excel. Learning how to use a completely new software tool will not be easier.

ADD REPLYlink written 2.9 years ago by igor11k

MS Excel does not change data. You need to format the excel cells as per your format.

ADD REPLYlink written 2.9 years ago by Renesh1.9k
1

Renesh's comment is not correct. Try the following: Open a worksheet. Type "MAR7". You'll see "7-Mar" as Excel formats your text as a date. Now correct the formatting to "text" (Format|Cells). You will see "7-Mar" become a number. On my Macintosh it's 42801. There is no way to recover the original text "MAR7". The data are changed.

ADD REPLYlink written 2.9 years ago by David Quigley11k
1

As I said, you need to format first the cells to type your data as you need. For example, select the column and change the formatting to Text. Now, type MAR7 and it will be displayed exactly as MAR7

ADD REPLYlink written 2.9 years ago by Renesh1.9k

Now imagine teaching that habit to many thousands of biologists around the world who still use Excel.

ADD REPLYlink written 2.9 years ago by Alex Reynolds30k

As with everything, you just have to know how to use it properly. If you want to preserve your data exactly as it is, open a blank Excel sheet, format all cells as text, and then paste your data into it as plain text. This prevents Excel from doing any automatic changes.

Unfortunately, however, even data on the Nature server that's associated with published work has these formatting issues.

Excel is a very powerful tool that anyone should be grateful for having. That said, as I get more skilled with awk and sed, I find that I need to use Excel less and less. In fact, I have not used it in the last year.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Kevin Blighe63k
1
gravatar for Pierre Lindenbaum
2.9 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

http://www.knime.org workbench

ADD COMMENTlink written 2.9 years ago by Pierre Lindenbaum129k
1
gravatar for Alex Reynolds
2.9 years ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

Unless you have regulatory issues to be worried about, you could use Google Sheets: https://www.google.com/sheets/about/

One advantage to doing work in the cloud with a tool like Google Sheets is that this makes your data easily shared with colleagues, and you can do collaborative and concurrent editing wherever you have a web browser and network connection available to you.

A disadvantage is that this makes your data easily shared with people who aren't your colleagues — as well as with Google, who have financial affiliations with companies like 23andMe etc. So keep this in mind if you are working with medical or proprietary data.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Alex Reynolds30k

Yes, and those online Word processors, etc, appear to be getting better over time. I used Word online completely for the first time last week (via my Outlook account). As you've implied, though, for things like clinical data, it may actually be against the law to host such data on a third-party server. Regulations differ per health system and nation, though.

ADD REPLYlink written 2.9 years ago by Kevin Blighe63k
0
gravatar for sacha
2.9 years ago by
sacha1.9k
France
sacha1.9k wrote:

Just found : http://csved.sjfrancke.nl/

ADD COMMENTlink written 2.9 years ago by sacha1.9k

I have not tried it myself but perhaps google sheets is another easy option without requiring another program install.

ADD REPLYlink written 2.9 years ago by genomax87k
0
gravatar for Friederike
2.9 years ago by
Friederike6.0k
United States
Friederike6.0k wrote:

GraphPad Prism is good for statistics and nice plots

Some stuff may also be done in Galaxy, depends on the question that needs to be addressed, but Galaxy basically give GUI-based access to many of the bash functions, such as cut, sed, even awk-like stuff.

ADD COMMENTlink written 2.9 years ago by Friederike6.0k

GraphPad Prism is commercial software and requires a license purchase.

ADD REPLYlink written 2.9 years ago by genomax87k

so does Excel, no? If the question implied only free solutions I missed that.

ADD REPLYlink written 2.9 years ago by Friederike6.0k

I generally like to know if software being mentioned/recommended on Biostars is freely available or requires a purchase. That was the reason I was only making a note that Prism is not free software.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by genomax87k
0
gravatar for h.mon
2.9 years ago by
h.mon30k
Brazil
h.mon30k wrote:

The most obvious Excel replacement is LibreOffice Calc. Two alternatives are pyspread and Tad.

ADD COMMENTlink written 2.9 years ago by h.mon30k

Are they known not to change gene names :)

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by genomax87k

I didn't test extensively, but as far as I noticed the genes usually changed by MSExcel (MARCH5, SEPT10, etc) are untouched. For me, they also have the advantage of not messing with scientific notation and decimals - which may happen due to some localization issue due to differences between my language locales and scietific standards.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by h.mon30k

I think that LibreOffice Calc is less forgiving that Excel, but in that sense it is better for people like us who need to know all changes that are happening to our data! I have been using Calc for the past year and I would say that it gets better when you learn how to use it.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Kevin Blighe63k
0
gravatar for igor
2.9 years ago by
igor11k
United States
igor11k wrote:

A lean and simple (only 218 bytes!) spreadsheet app: http://xem.github.io/sheet/

Free, open source, and no extra crud to mess up dates!

ADD COMMENTlink written 2.9 years ago by igor11k
0
gravatar for Renesh
2.9 years ago by
Renesh1.9k
United States
Renesh1.9k wrote:

MS Excel is not a good tool for data analysis unless you have small-scale data. To manipulate tables efficiently and considering large-scale datasets, it is always better to use databases like MySQL or Psql which are open source and easy to use. You can also manipulate these databases through scripting and statistical languages like Python, R etc.

ADD COMMENTlink written 2.9 years ago by Renesh1.9k

I m just wondering if it's possible to index a tabular text file to have random access ...

ADD REPLYlink written 2.9 years ago by sacha1.9k

Yes you can index tabular files in MySQL or Psql

ADD REPLYlink written 2.9 years ago by Renesh1.9k

I m stupid... tabix do that !

ADD REPLYlink written 2.9 years ago by sacha1.9k

and tribble (gatk/picard=

ADD REPLYlink written 2.9 years ago by Pierre Lindenbaum129k

Greate! Let's look which gui viewer support index file to load and edit large dataset

ADD REPLYlink written 2.9 years ago by sacha1.9k
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