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318 results • Page 3 of 7
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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 9 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 3.2 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
4.3k
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
934
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
1.4k
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
71
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 ▴ 760
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 3.6 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
176k
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 4.4 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 4.5 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
4.3k
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
941
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
Answer: Generate Read counts from bam file
Comment: Generate Read counts from bam file
C: Heatmap : why scaling ?
Answer: How do I download a list of genes involved in cellular metabolism (in humans) ba
A: Incomplete reactome.org all pathway level to ENSEMBL ID annotation files
Comment: p-value combination methods
Comment: p-value combination methods
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Recent Replies
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT by tw_140 • 0
Thank you, I really appreciate your insight! I will look into the dropouts I have.
Answer: Generate Read counts from bam file by NextGenSeek • 0
Are you analysing RNA or DNA heteroplasmy levels?
Comment: What type of cancer did they study in this paper? by GenoMax 136k
Perhaps the exact cancer type is not what is important. Looks like they are [**all solid tumors**][1] with a baseline sample and one after …
Comment: p-value combination methods by i.sudbery 18k
edgeR *is* an NB-GLM. The input to NB-GLMs, including edgeR and DESeq is read counts from each sample.
Answer: What type of cancer did they study in this paper? by jared.andrews07 ★ 16k
Cutaneous or ocular melanoma. It's from [this paper](https://aacrjournals.org/cancerimmunolres/article/10/2/162/678013/NKG7-Is-a-T-cell-Int…
Comment: p-value combination methods by sehriban.buyukkilic • 0
its output of edgeR. I'm asking for input of NB-GLM? what should be input of it?
Comment: How do I download a list of genes involved in cellular metabolism (in humans) ba by el24 ▴ 40
Hi @pratik, Thanks for the helpful solution above. I'm working on a similar task in Mouse species and noticed the CTD database is human-spe…
Comment: Match variants for allele frequency, LD score, and other features by Jautis ▴ 520
Trying to bump this
Comment: p-value combination methods by i.sudbery 18k
The parameters you have here are the *output* of an NB-GLM, not the input to an NB-GLM (most likely edgeR?)
Comment: How can I adjust Y-axis scale when making relative abundance box plot ? by ATpoint 78k
Please provide data as dput(), not via any random dropbox, that could be anything (also malware, theoretically). If log transformation crea…
Comment: Extracting chimeric reads from mapping by doggie • 0
Hi Pierre, so does samjdk support single-end reads for extracting chimeric reads? I've aligned my virus to the human reference, sorted the …
Comment: How can I adjust Y-axis scale when making relative abundance box plot ? by dthorbur ▴ 870
You can try `scale_y_sqrt()` instead if you don't like the look of the log10 transformation. As an aside, it doesn't look like your fill va…
Comment: Making multiple box plots with relative abundance in R by ohtang7 ▴ 30
Thank you!! I really appreciate your help.
Comment: Making multiple box plots with relative abundance in R by rpolicastro 12k
In `scale_fill_manual` you have e.g. `"stray"` but in your data it's `"Stray"`. Just make sure the cases match.
Comment: How to use conumee segment mean for gistic input by sativus ▴ 10
Did you manage to find an answer to this question, i have done so myself, but would like to confirm that this methodology is sound?
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