Limit : this year
all time today this week this month this year
318 results • Page 3 of 7
Sort: Rank
Rank Views Votes Replies
24
votes
4
replies
7.1k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 8 months ago by 41k • written 4.3 years ago by 78k
15
votes
4
replies
4.4k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 8 months ago by 41k • written 3.3 years ago by ▴ 340
26
votes
0
replies
2.3k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
interpretation cancer annotation variant
updated 8 months ago by 41k • written 4.1 years ago by 19k
10
votes
1
reply
2.2k
views
Tutorial: introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
SARS-CoV-2 fastv COVID-19
updated 8 months ago by 41k • written 3.7 years ago by ★ 2.5k
60
votes
52
replies
42k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 8 months ago by 41k • written 7.2 years ago by ★ 3.4k
13
votes
7
replies
5.6k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 8 months ago by 41k • written 3.2 years ago by 86k
18
votes
22
replies
8.4k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 10 weeks ago by ▴ 20 • written 4.0 years ago by 8.4k
0
votes
0
replies
1.0k
views
Tutorial: BrainArray CDF, annotation, etc
db brainarray cdf
updated 8 months ago by 41k • written 3.2 years ago by 86k
12
votes
0
replies
2.5k
views
Tutorial: Long versus wide data for plotting genomics data in R.
ggplot2 tidyverse data.table R
updated 8 months ago by 41k • written 3.3 years ago by 12k
76
votes
70
replies
18k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 8 months ago by 41k • written 5.8 years ago by 86k
1
vote
1
reply
1.3k
views
Tutorial: Downloading GnuWin and using to convert txt to bed file for windows users
bed bed2txt sequencing txt
updated 8 months ago by 41k • written 3.3 years ago by • 0
4
votes
3
replies
4.4k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 8 months ago by 41k • written 5.6 years ago by ★ 3.9k
4
votes
1
reply
1.3k
views
Tutorial: Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
BED BEDtools
updated 8 months ago by 41k • written 3.3 years ago by ▴ 40
3
votes
0
replies
3.4k
views
Tutorial: Sorting GFF/GTF files
gtf gff
updated 8 months ago by 41k • written 3.4 years ago by 8.4k
20
votes
6
replies
5.3k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 8 months ago by 41k • written 7.2 years ago by ★ 5.2k
2
votes
2
replies
1.9k
views
Tutorial: Human mitochondrial DNA annotation in SnpEff
chrMT SNP snpEff
updated 8 months ago by 41k • written 3.4 years ago by 3.2k
12
votes
5
replies
2.2k
views
Tutorial: FASTA file split
fasta
updated 8 months ago by 41k • written 3.5 years ago by 8.4k
0
votes
0
replies
1.6k
views
Tutorial: VIDEO: Installing BLAST Databases on Your Own Computer
BLAST-databases Linux sequence MacOSX
updated 8 months ago by 41k • written 3.5 years ago by ▴ 450
0
votes
0
replies
938
views
Tutorial: VIDEO: BLAST Searches Through a Data Science Lens
Covid19 Data-Science sequence BLAST
updated 8 months ago by 41k • written 3.5 years ago by ▴ 450
2
votes
1
reply
1.5k
views
Tutorial: A very simple way to detect viruses and microorganisms from mNGS FASTQ data using fastv
SARS-CoV-2 fastv COVID-19 viruses
updated 8 months ago by 41k • written 3.5 years ago by ★ 2.5k
72
votes
26
replies
27k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 9 months ago by 41k • written 9.8 years ago by 99k
59
votes
43
replies
20k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 8 months ago by 41k • written 6.2 years ago by ★ 1.4k
20
votes
7
replies
6.1k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 8 months ago by 41k • written 5.1 years ago by ▴ 770
4
votes
0
replies
1.7k
views
Tutorial: NIH CDE browser for TCGA clinical data CDE codes
nih tcga metadata cde
updated 8 months ago by 41k • written 3.7 years ago by 86k
10
votes
4
replies
11k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 8 months ago by 41k • written 4.4 years ago by 5.7k
0
votes
0
replies
1.2k
views
Tutorial: Training GeneMark-EP+ ab-initio tool
abinitio training genemark annotation
updated 8 months ago by 41k • written 3.8 years ago by 8.4k
2
votes
1
reply
2.9k
views
Tutorial: How to extract and filter SNP data from the genotyping-by-sequencing (GBS) data in vcf format using bcftools
bcftools SNP-Filtering VCF
updated 8 months ago by 41k • written 3.8 years ago by ▴ 10
5
votes
0
replies
3.1k
views
Tutorial: How to run CWL with Nextflow
cwl nextflow
updated 8 months ago by 41k • written 3.8 years ago by ★ 3.4k
5
votes
2
replies
2.2k
views
Tutorial: Using Bedtools Closest (closestBed) to make distance histograms of protein binding frequency near all types of pre-RNA junctions (e.g. exon-intron an…
preRNA closestBed bedtools-closest bedtools
updated 8 months ago by 41k • written 4.8 years ago by ▴ 10
50
votes
3
replies
4.5k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 8 months ago by 41k • written 4.9 years ago by 78k
21
votes
9
replies
6.3k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 9 months ago by 41k • written 10.5 years ago by 9.7k
282
votes
39
replies
177k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 8 months ago by 41k • written 9.3 years ago by 20k
64
votes
26
replies
13k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 8 months ago by 41k • written 6.2 years ago by 86k
34
votes
15
replies
6.0k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 8 months ago by 41k • written 4.5 years ago by ★ 9.3k
20
votes
4
replies
2.5k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 8 months ago by 41k • written 4.6 years ago by ▴ 180
14
votes
7
replies
6.1k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 8 months ago by 41k • written 7.5 years ago by ★ 3.4k
2
votes
0
replies
4.4k
views
Tutorial: Calculation of TSS Scores for ATAC-seq Data
next-gen-sequencing
updated 8 months ago by 41k • written 4.4 years ago by ▴ 20
0
votes
0
replies
1.0k
views
Tutorial: Apply ALoFT to identify loss-of-function somatic or germline variants
ALoFT
updated 8 months ago by 41k • written 4.5 years ago by ★ 9.3k
16
votes
11
replies
14k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 8 months ago by 41k • written 7.1 years ago by ★ 4.7k
10
votes
5
replies
21k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 8 months ago by 41k • written 5.4 years ago by ★ 9.3k
34
votes
15
replies
19k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 8 months ago by 41k • written 7.2 years ago by ▴ 310
6
votes
3
replies
4.4k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 8 months ago by 41k • written 5.1 years ago by ▴ 40
0
votes
0
replies
1.0k
views
Tutorial: Introduction to Gen3 Webinar
gen3 open-source data-commons big-data
updated 8 months ago by 41k • written 4.8 years ago by ▴ 310
0
votes
1
reply
1.3k
views
Tutorial: SFA (Stochastic Frontier Analysis) Frontier 4.1
r spss
updated 8 months ago by 41k • written 5.8 years ago by ▴ 10
4
votes
2
replies
3.5k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 8 months ago by 41k • written 7.8 years ago by ★ 2.5k
28
votes
4
replies
4.1k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 8 months ago by 41k • written 4.9 years ago by 26k
61
votes
6
replies
9.3k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 9 months ago by 41k • written 10.3 years ago by 9.7k
4
votes
0
replies
945
views
Tutorial: Finding individual motif occurrences with FIMO from the MEME suite
motif meme jaspar fimo
updated 8 months ago by 41k • written 5.0 years ago by 78k
5
votes
2
replies
2.2k
views
Tutorial: NCBI submissions: SRA and TSA
NCBI TSA SRA RNA-Seq
updated 8 months ago by 41k • written 5.0 years ago by ▴ 50
6
votes
0
replies
1.5k
views
Tutorial: NCBI dbVar releases updated human reference structural variation (SV) data files and tutorials
dbvar structural-variation
updated 8 months ago by 41k • written 5.0 years ago by ▴ 70
318 results • Page 3 of 7
Recent Votes
Comment: Problematic fastq files...How can we trust them?
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: An incomprehensible error with R package gggenes
Recent Locations • All
Bologna, 7 minutes ago
Spain, 10 minutes ago
Hungary, 10 minutes ago
Italy, 13 minutes ago
United States, 15 minutes ago
Frankrike, 24 minutes ago
Tehran, 32 minutes ago
Recent Awards • All
Popular Question to endre.sebestyen ▴ 10
Popular Question to beausoleilmo ▴ 560
Commentator to Brian Bushnell 19k
Popular Question to Gama313 ▴ 120
Popular Question to nanodano ▴ 30
Popular Question to shome ▴ 10
Popular Question to Malachi Griffith 19k
Recent Replies
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with by GenoMax 136k
Yes that should be true. I will let https://www.biostars.org/u/14684/ confirm.
Comment: From TPM to raw counts by Gama313 ▴ 120
Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link: A= …
Comment: From TPM to raw counts by Gama313 ▴ 120
Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
Answer: Are 10x cellranger-arc ATAC bam files deduplicated? by swbarnes2 13k
My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo by fluke • 0
Thanks a lot for your answer, I’m confused between RSEM expected count and RSEM normalized count. I’m working on this dataset from UCSC ht…
Answer: From TPM to raw counts by Istvan Albert 99k
In principle, the TPM formula can be reverted, see the timeless post * [What the FPKM? A review of RNA-Seq expression units][1] In p…
Comment: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S by beausoleilmo ▴ 560
You're right, I wasn't explaining the problem clearly. Thanks for the directions! - The depth; coverage ~3.00X ± 2.50 SD - The sequen…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Mensur Dlakic ★ 25k
All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo by CTLong ▴ 20
Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
Comment: How to obtain data on the coordinates of the Exon region from UCSC by ayasu • 0
Sorry for the delay in expressing my thanks. I found the advice to look at the information from MySQL very useful. I will also refer to t…
Comment: From TPM to raw counts by Brian Bushnell 19k
I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Brian Bushnell 19k
In most cases error-correction should take care of error-spawned fake minor alleles, though... > If you want to convince yourself of this,…
Answer: Using metagenome assembly and binning to identify and mitigate contamination in by Mensur Dlakic ★ 25k
It is a valid question, and I particularly like when posters err on the side of providing more than less detail. Metagenomic binning can be…
Answer: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S by Brian Bushnell 19k
I don't understand your plot. Perhaps a legend would help? I also don't know what you mean by "genotype frequency"; is that the ratio of …
Comment: Does GNOMAD use all LOFTEE LoF filters? by AMARU • 0
Can you post the commands you used? I am having some issues running that plugin on vep v110. It appears in fields but it doesn't annotat…
Traffic: 803 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6