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18 results • Page
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3
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2.1k
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News:
New ebook: From cell line to Command line to learn computational biology
unix
snakemake
computational-biology
RNA-seq
8 days ago by
Ming Tommy Tang
★ 3.6k
0
votes
3
replies
997
views
News:
:: FINAL CALL :: A Practical Introduction to NGS Data Analysis (Nov 29 - Dec 1, 2023 in Munich, Germany) - only 2 seats left
DNA-Seq
NGS
RNA-Seq
Workshop
14 days ago by
David Langenberger
10k
3
votes
0
replies
239
views
News:
gnomAD v4 released
gnomad
27 days ago by
Pierre Lindenbaum
158k
0
votes
0
replies
189
views
News:
Spatial Omics and Multiplexed Image Analysis course
Spatial-Omics
Multiplexed-Image-Analysis
updated 29 days ago by
Ram
41k • written 29 days ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
180
views
News:
Virtual de novo RNA-seq (transcriptomics) Workshop: November 13-16, 2023
workshop
RNA-seq
transcriptomics
updated 29 days ago by
Ram
41k • written 29 days ago by
mia.nahom
▴ 10
0
votes
0
replies
178
views
News:
Next-Generation Sequencing Data Analysis: A Practical Introduction (Nov 29 – Dec 1 in Munich, Germany)
RNAseq
DNAseq
NGS
Workshop
11 days ago by
Lars
★ 1.0k
0
votes
0
replies
177
views
News:
Course - Introduction to Machine Learning in R
R
Statistical-Learning
Omics
Machine-Learning
updated 27 days ago by
Ram
41k • written 27 days ago by
carlopecoraro2
★ 2.4k
1
vote
0
replies
173
views
News:
course - Advanced Python Programming
Python-Programming
updated 20 days ago by
Ram
41k • written 20 days ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
166
views
News:
GWAS course
R
Bioinformatics
GWAS
5 days ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
152
views
News:
GWAS course
R
GWAS
updated 20 days ago by
Ram
41k • written 20 days ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
152
views
News:
Course. - Computational Tumor Evolution
TumorEvolution
CancerGenomics
Bioinformatics
11 days ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
149
views
News:
Genemod - Lab Management Software
lab-management-software
research
updated 15 days ago by
Ram
41k • written 16 days ago by
Genemod
• 0
0
votes
0
replies
145
views
News:
Course: Genome Assembly using Oxford Nanopore Sequencing
GenomeAssembly
Nanopore
Bioinformatics
16 days ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
140
views
News:
Course - Introduction to Bayesian Data Analysis
R
Statistics
RegressionModeling
Bayesian
23 days ago by
carlopecoraro2
★ 2.4k
3
votes
0
replies
131
views
News:
NCBI BLAST+ 2.2.15 now available for download
NCBI
Taxonomy
BLAST
7 days ago by
PeterC_NCBI
▴ 370
0
votes
0
replies
115
views
News:
Online expert taught RNA-Seq workshop
workshop
7 days ago by
fturner
▴ 10
0
votes
0
replies
115
views
News:
Course - RNAseq in non-model organisms
Pacbio
RNAseq
Nanopore
8 days ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
108
views
News:
Course - Introduction to R Shiny
R
Shiny
DataVisualisation
7 days ago by
carlopecoraro2
★ 2.4k
18 results • Page
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Comment: SPAdes error: finished abnormally, OS return value: 21
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
Comment: unicycler error : [Errno 13] Permission denied:
Comment: unicycler error : [Errno 13] Permission denied:
Answer: SPAdes error: finished abnormally, OS return value: 21
Comment: SPAdes error: finished abnormally, OS return value: 21
Removing UMI with UMI tools?
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Recent Replies
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
GeneBC12
• 0
Thanks GenoMax for the reply. That being said, does this difference in total bases between read1 and read2 have an effect in subsequent rea…
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters
by
DINESHR
• 0
Here are my PCA results plotted through Diffbind and Correlation heat map by deeptools shows some clustering in the samples @atpoint ![e…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
by
dsull
★ 5.0k
Yeah, sometimes it looks "prettier" to plot p-value rather than adjusted p-value; although either one is technically ok to plot (even multi…
Comment: How to get unaligned reads and aligned reads into separate files from SAM/BAM?
by
rpolicastro
12k
I suppose if you really wanted to do it in one pass pysam would be an option. Courtesy of ChatGPT with a few modifications, and tested to s…
Comment: frequency plot for peaks
by
Ankit
▴ 400
what is your txdb? can you explain your experiment in detail?
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when
by
cmdcolin
★ 3.4k
paste the file in csv format and a R wizard might come along and help :)
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when
by
rpolicastro
12k
Your intuition was correct. You want to make two separate data frames and join them on sample name. This code is untested but will probably…
Comment: Generate Read counts from bam file
by
ATpoint
78k
It has nothing to do with low complexity. You always map to the entire genome since the reads can come from the entire genome. If you take …
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters
by
ATpoint
78k
DiffBind uses DESeq2 for differential analysis and its method to moderate logFCs. When noise is high and there is little evidence for diffe…
Comment: p-value combination methods
by
dsull
★ 5.0k
Was this response written by a LLM? It's a useful response but it doesn't really answer the initial question... In response to the OP ques…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
by
RNAseqer
▴ 250
Well, because I want to also draw attention to nominally significant genes as they are subjected to follow up experiments and would be nice…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
by
Nitin Narwade
★ 1.5k
Actually, to add an **EXACT line/mark** for one value based on another is impossible (for me at least). What you can do is, select the min…
Comment: Construction of single sequence assembly out of contigs
by
analyst
▴ 10
Thanks colindaven!
Comment: Generate Read counts from bam file
by
Enrique
• 0
Great appreciation. If you don't use restrictive arguments in the mapping, is better to use the entire genome to avoid the false positives …
Comment: Generate Read counts from bam file
by
ATpoint
78k
No, absolutely not. Mapping to such a tiny subset leads to false positives. Use the entire genome that includes the mt reference.
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