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11 results • Page
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News:
Online Training - Bioinformatics Pipeline Development with Nextflow (November 15-17, 2023)
nextflow
automation
pipeline
development
42 minutes ago by
David Langenberger
10k
1
vote
0
replies
64
views
News:
Successful NCBI NIAID Codeathon on VCF Files in SARS-CoV-2 Genomics
NCBI
Codeathon
15 hours ago by
PeterC_NCBI
▴ 330
0
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123
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News:
Introduction to Nextflow (2 seats left)
Nextflow
Workflow
Reproducibility
updated 3 days ago by
Ram
40k • written 3 days ago by
carlopecoraro2
★ 2.3k
0
votes
0
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105
views
News:
course - Population Genomics Using Ancient DNA Data
Bioinformatics
PopulationGenomics
Genomics
aDNA
4 days ago by
carlopecoraro2
★ 2.3k
0
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2
replies
541
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News:
The Practice of RADseq: Population Genomics Analysis with Stacks (RADS02) Early bird deadline approaching - 20th September
population-genomics
radseq
stacks
updated 2 days ago by
Dave Carlson
★ 1.4k • written 3 days ago by
oliverhooker
▴ 110
0
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0
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80
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News:
Workshop - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (November 8-10, 2023 in Berlin)
workshop
scRNA-Seq
RNA-Seq
single-cell
updated 17 hours ago by
Ram
40k • written 1 day ago by
David Langenberger
10k
0
votes
0
replies
126
views
News:
Online Course - A Practical Introduction to NGS Data Analysis - October 23-25, 2023
DNA-seq
RNA-seq
Workshop
updated 2 days ago by
Ram
40k • written 2 days ago by
David Langenberger
10k
0
votes
0
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124
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News:
Course - GLMMs in R
GLMM
Mixed-Models
updated 3 days ago by
Ram
40k • written 3 days ago by
carlopecoraro2
★ 2.3k
0
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0
replies
118
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News:
Course: Data Manipulation and Visualisation with Python
Python
Data-Visualization
Data-Manipulation
updated 2 days ago by
Ram
40k • written 2 days ago by
carlopecoraro2
★ 2.3k
0
votes
0
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123
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News:
Genomic Prediction course
Bioinformatics
GWAS
GenomicPrediction
4 days ago by
carlopecoraro2
★ 2.3k
0
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0
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82
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News:
Research Breakthrough in Identifying Viral Escape Mutations for Improved Therapeutic Design
sequence-analysis
sars-cov-2
spike-protein
updated 18 hours ago by
Ram
40k • written 1 day ago by
Prem
• 0
11 results • Page
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A: Using repeat region filter post QC
Online Training - Bioinformatics Pipeline Development with Nextflow (November 15-17, 2023)
Unsupervised clustering on gene expression data
Answer: Identifying common DEGs among multiple datasets
Answer: Identifying common DEGs among multiple datasets
A: what do the headers of the rMATS output files mean?
A: what do the headers of the rMATS output files mean?
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Answer: How to check RNAseq support for annotated genes?
by
Michael
53k
To check for support of gene models by RNAseq, there are several proven workflows. I recommend using them all: - Standard RNAseq analysis …
Comment: ATAC-seq troubleshoot - Just Noise
by
ATpoint
76k
Yes, definitely lots of noise and few peaks for such an experiment. Which celltype is that, and which lab protocol did you use?
Comment: DESeq2 analysis using two featureCounts generated from different studies
by
abedkurdi10
▴ 190
What do you mean by gene lists?
Comment: Find potential important genes from bulk-RNA seq experiment
by
Michael
53k
You can use e.g. the WGCNA package for network analysis. In your case multiple samples this might mean multiple patients or a time series o…
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
by
Edoardo
• 0
Thank you so much for your responses. @genomax , I've downloaded both of the databases you recommended. I attempted to combine them into …
Answer: Simulate short-read RNA-seq data from long-read RNA-seq data
by
Mensur Dlakic
★ 24k
I think you could try doing this, but it wouldn't be appropriate. You'd be bringing long-read errors, which I believe are higher than short…
Comment: Salmon index not progressing
by
camillab.
▴ 130
I opened tow terminals and one was the code to build a decoy-aware transcriptome and the other was building indexes (no decoy)
Comment: Adding a control sample to bulk RNA-seq
by
Chris
▴ 180
Thank you for the explanation! So just want to confirm one control with replicate is totally useless even can't use as a reference?
Answer: DESeq2 analysis using two featureCounts generated from different studies
by
swbarnes2
13k
Comparing samples between labs is a bad idea. Better to generate gene lists from one study from one lab, and gene lists from another study…
Comment: Adding a control sample to bulk RNA-seq
by
swbarnes2
13k
If a sample wasn't prepared along side your treated samples, it is a different batch. If you had treated and controls in each of two diffe…
Comment: kallisto normalized TPM values without bootstraps
by
ATpoint
76k
You don't need sleuth. Typically these deconvolutions, or most downstream analysis, is done on the gene- rather than the transcript-level w…
Comment: Salmon index not progressing
by
ATpoint
76k
If the top $CPU column shows some values in the hundreds then it is doing something (actually when it's > 0%). So based on the screenshot i…
Comment: Salmon index not progressing
by
camillab.
▴ 130
Thank you. Waiting it's not gonna hurt me, when should I stop hoping and give up is the question? do you know is there a way if I can see i…
Comment: Filtering VCF to divide with equal sizes
by
Ram
40k
A more efficient way would be to make a 2 column CSV file, one column with the count value and the other with the chr:start-end range, then…
Answer: Filtering VCF to divide with equal sizes
by
avelarbio46
▴ 30
I divided my contigs using R, but it was more complex than the program Pierre Lindenbaum made (https://jvarkit.readthedocs.io/en/latest/Vcf…
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