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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
Ram
41k • written 4.3 years ago by
ATpoint
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
Ram
41k • written 3.3 years ago by
Thind amarinder
▴ 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
Ram
41k • written 4.1 years ago by
Malachi Griffith
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
Ram
41k • written 3.7 years ago by
chen
★ 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
Ram
41k • written 7.2 years ago by
steve
★ 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
Ram
41k • written 3.2 years ago by
Kevin Blighe
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
evoecogen
▴ 20 • written 4.0 years ago by
Juke34
8.4k
0
votes
0
replies
1.0k
views
Tutorial:
BrainArray CDF, annotation, etc
db
brainarray
cdf
updated 8 months ago by
Ram
41k • written 3.2 years ago by
Kevin Blighe
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
Ram
41k • written 3.2 years ago by
rpolicastro
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
Ram
41k • written 5.8 years ago by
Kevin Blighe
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
Ram
41k • written 3.3 years ago by
opheevallee
• 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
Ram
41k • written 5.6 years ago by
Daniel
★ 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
Ram
41k • written 3.3 years ago by
sdsubaru33
▴ 40
3
votes
0
replies
3.4k
views
Tutorial:
Sorting GFF/GTF files
gtf
gff
updated 8 months ago by
Ram
41k • written 3.4 years ago by
Juke34
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
Ram
41k • written 7.2 years ago by
Denise CS
★ 5.2k
2
votes
2
replies
1.9k
views
Tutorial:
Human mitochondrial DNA annotation in SnpEff
chrMT
SNP
snpEff
updated 8 months ago by
Ram
41k • written 3.4 years ago by
Arup Ghosh
3.2k
12
votes
5
replies
2.2k
views
Tutorial:
FASTA file split
fasta
updated 8 months ago by
Ram
41k • written 3.5 years ago by
Juke34
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
Ram
41k • written 3.5 years ago by
brian.fristensky
▴ 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
Ram
41k • written 3.5 years ago by
brian.fristensky
▴ 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
Ram
41k • written 3.5 years ago by
chen
★ 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
Ram
41k • written 9.8 years ago by
Istvan Albert
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
Ram
41k • written 6.2 years ago by
Rox
★ 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
Ram
41k • written 5.1 years ago by
ahmad mousavi
▴ 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
Ram
41k • written 3.6 years ago by
Kevin Blighe
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
Ram
41k • written 4.4 years ago by
colindaven
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
Ram
41k • written 3.8 years ago by
Juke34
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
Ram
41k • written 3.8 years ago by
Asad Prodhan
▴ 10
5
votes
0
replies
3.1k
views
Tutorial:
How to run CWL with Nextflow
cwl
nextflow
updated 8 months ago by
Ram
41k • written 3.8 years ago by
steve
★ 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
Ram
41k • written 4.8 years ago by
linuxborg2
▴ 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
Ram
41k • written 4.9 years ago by
ATpoint
78k
21
votes
9
replies
6.3k
views
8 follow
Tutorial:
Interactive Perl Learning
perl
updated 9 months ago by
Ram
41k • written 10.5 years ago by
Medhat
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
Ram
41k • written 9.3 years ago by
Obi Griffith
20k
64
votes
26
replies
13k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 8 months ago by
Ram
41k • written 6.2 years ago by
Kevin Blighe
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
Ram
41k • written 4.4 years ago by
Shicheng Guo
★ 9.3k
20
votes
4
replies
2.5k
views
Tutorial:
Bash One-liners collection on Github
bash
linux
shell
updated 8 months ago by
Ram
41k • written 4.5 years ago by
nim.1111.ou
▴ 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
Ram
41k • written 7.5 years ago by
steve
★ 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
Ram
41k • written 4.4 years ago by
Sael
▴ 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
Ram
41k • written 4.5 years ago by
Shicheng Guo
★ 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
Ram
41k • written 7.1 years ago by
TriS
★ 4.7k
10
votes
5
replies
21k
views
Tutorial:
Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 8 months ago by
Ram
41k • written 5.4 years ago by
Shicheng Guo
★ 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
Ram
41k • written 7.2 years ago by
martinguerrerog89
▴ 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
Ram
41k • written 5.1 years ago by
contact
▴ 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
Ram
41k • written 4.8 years ago by
Danielle
▴ 310
0
votes
1
reply
1.3k
views
Tutorial:
SFA (Stochastic Frontier Analysis) Frontier 4.1
r
spss
updated 8 months ago by
Ram
41k • written 5.8 years ago by
helgasaraswati
▴ 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
Ram
41k • written 7.8 years ago by
chen
★ 2.5k
28
votes
4
replies
4.1k
views
Tutorial:
Modern Statistics for Modern Biology
statistics
updated 8 months ago by
Ram
41k • written 4.9 years ago by
Jean-Karim Heriche
26k
61
votes
6
replies
9.3k
views
Tutorial:
Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 9 months ago by
Ram
41k • written 10.3 years ago by
Medhat
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
Ram
41k • written 5.0 years ago by
ATpoint
78k
5
votes
2
replies
2.2k
views
Tutorial:
NCBI submissions: SRA and TSA
NCBI
TSA
SRA
RNA-Seq
updated 8 months ago by
Ram
41k • written 5.0 years ago by
saraoppenheim
▴ 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
Ram
41k • written 5.0 years ago by
lonphan
▴ 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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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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