User: boczniak767

gravatar for boczniak767
boczniak767690
Reputation:
690
Status:
Trusted
Location:
Poland
Last seen:
1 week, 6 days ago
Joined:
8 years, 10 months ago
Email:
m*************@protonmail.ch

Posts by boczniak767

<prev • 142 results • page 1 of 15 • next >
0
votes
1
answer
323
views
1
answers
Comment: C: Reactome Plant to Cytoscape - possible?
... I'm working on maize and Plant Reactome has maize IDs (version 4). So I don't have to map my genes. ...
written 13 days ago by boczniak767690
0
votes
1
answer
1.6k
views
1
answers
Comment: C: ADMIXTURE download page down. Mirror?
... This happened again, not sure it is the same thing, but here is the link [link][1] [1]: https://dnagenics.com/admixture-ucla-human-genetics/ ...
written 3 months ago by boczniak767690
0
votes
0
answers
203
views
0
answers
Comment: C: Clustering of log-fold change with zeros
... The problem is that the majority of data are zeros. There are no (or very few) rows (genes) with significant data for all columns (projects). Full set has ca. 10 columns, I could use smaller set of five, but the problem remains. ...
written 7 months ago by boczniak767690
0
votes
0
answers
203
views
0
answers
Clustering of log-fold change with zeros
... Hi all, I have made a table of log2 fold change ratios from several microarray studies. For genes without statistically significant change I typed `0` (there are many such cases), other values are just log2 fold changes. My question is, if it is possible to make clustering of such data? I could, o ...
gene expression clustering written 7 months ago by boczniak767690
0
votes
0
answers
115
views
0
answers
Compare MN-ase and FAIRE-seq/DNA-se results
... Hi all, I'm wondering if it is possible to compare MN-ase and FAIRE (or DN-ase) results. I tried to compare it using `bedtools intersect -v` to count features shared and not-shared between files. In theory, MN-ase gives opposite results to FAIRE or DN-ase. So great number of not shared features wo ...
dna-se faire mn-ase written 8 months ago by boczniak767690
0
votes
0
answers
241
views
0
answers
homer IDR, pseudoreplicates error
... Hi all, I'm trying the IDR procedure for FAIRE-seq peaks generated with Homer The procedure is outlined here [homer-idr][1] [1]: https://github.com/karmel/homer-idr#using-homer-idr It works ok till step 5. Using command as in example `python run_idr.py pseudoreplicate -d [tag_dirs to split] ...
homer idr faire written 9 months ago by boczniak767690
1
vote
1
answer
309
views
1
answers
Answer: A: Cytoscape, cannot delete column
... Ok, so I managed to do what I needed. Maybe for someone it would be useful. In short: 1. I unpacked the `cys` file and renamed to `zip` 2. In `tables` subdirectory I searched files with instances of "DAP" (the part of a columns' name, which I wanted to delete) and writeit to file `grep -rl 'DAP ...
written 11 months ago by boczniak767690
0
votes
2
answers
8.3k
views
2
answers
Answer: A: Remove Illumina TruSeq Index adapters
... Check-out the Trimmomatic and `ILLUMINACLIP` function. It has a library for different TruSeq adapters which you specify in command. ...
written 12 months ago by boczniak767690
2
votes
1
answer
309
views
1
answer
Cytoscape, cannot delete column
... Hi, I have a problem with deleting columns in one of the networks in Cytoscape file. Formerly the session file was big, with huge network from which I separated few small. I also used Dynet app to compare the networks and this generated new columns. Then I deleted majority of networks to create sm ...
cytoscape written 12 months ago by boczniak767690
0
votes
6
answers
42k
views
6
answers
Comment: C: Estimate Insert Size In Paired-End/Mate-Pair
... It gives strange results for mean, and I don't know why. For my sam file, for 10000 lines it gives 217 (picard gives 198). This script for all reads gives 1032,79. Overall it seems that the value increases along with the read number. Edit. Other, smaller, file. Picard mean = 156 Qualimap and menti ...
written 12 months ago by boczniak767690

Latest awards to boczniak767

Popular Question 3 months ago, created a question with more than 1,000 views. For Grow/shrink ranges in bed file to a specified length
Popular Question 6 months ago, created a question with more than 1,000 views. For Interpro Enrichment - Any Organism
Popular Question 7 months ago, created a question with more than 1,000 views. For Interpro Enrichment - Any Organism
Scholar 11 months ago, created an answer that has been accepted. For A: Cytoscape, cannot delete column
Popular Question 18 months ago, created a question with more than 1,000 views. For FAIRE-seq optimal coverage - large genome
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Interpro Enrichment - Any Organism
Popular Question 2.6 years ago, created a question with more than 1,000 views. For FAIRE-seq optimal coverage - large genome
Centurion 3.2 years ago, created 100 posts.
Popular Question 3.3 years ago, created a question with more than 1,000 views. For [Excel 2003] Heatmap, Keep Color Only
Great Question 3.5 years ago, created a question with more than 5,000 views. For [Excel 2003] Heatmap, Keep Color Only
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Tools To Find Gene Ontology Term Enrichment
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Interpro Enrichment - Any Organism
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Tools To Find Gene Ontology Term Enrichment
Popular Question 5.7 years ago, created a question with more than 1,000 views. For [Excel 2003] Heatmap, Keep Color Only
Popular Question 5.9 years ago, created a question with more than 1,000 views. For [Excel 2003] Heatmap, Keep Color Only
Popular Question 6.2 years ago, created a question with more than 1,000 views. For [Excel 2003] Heatmap, Keep Color Only
Teacher 6.2 years ago, created an answer with at least 3 up-votes. For A: Transcription Factor Enrichment
Voter 6.5 years ago, voted more than 100 times.
Supporter 6.5 years ago, voted at least 25 times.
Teacher 7.7 years ago, created an answer with at least 3 up-votes. For A: Workflows For Microarray Meta-Analysis Projects.
Appreciated 7.7 years ago, created a post with more than 5 votes. For A: Workflows For Microarray Meta-Analysis Projects.
Good Answer 7.7 years ago, created an answer that was upvoted at least 5 times. For A: Workflows For Microarray Meta-Analysis Projects.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1037 users visited in the last hour