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411 results • Page
4 of 9
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6
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10
replies
5.2k
views
Tutorial:
Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR
dna-methylation
updated 13 months ago by
Ram
43k • written 6.2 years ago by
dec986
▴ 370
43
votes
6
replies
12k
views
Tutorial:
Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl
maf
tcga
vcf
updated 14 months ago by
Ram
43k • written 10.3 years ago by
Cyriac Kandoth
6.0k
5
votes
3
replies
5.4k
views
Tutorial:
bam2rpkm by bedtools
bam
RNA-Seq
bedtools
rpkm
updated 13 months ago by
toxin08x
• 0 • written 6.5 years ago by
jmzeng1314
▴ 130
16
votes
11
replies
8.3k
views
Tutorial:
How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta
how-to
documentation
13 months ago by
Ram
43k
106
votes
6
replies
26k
views
6 follow
Tutorial:
Creating workflows with snakemake and conda
workflow
snakemake
conda
updated 13 months ago by
Ram
43k • written 5.7 years ago by
finswimmer
16k
18
votes
40
replies
18k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 3.8 years ago by
krishdb38
• 0 • written 7.9 years ago by
Esaie
▴ 170
24
votes
4
replies
7.7k
views
Tutorial:
Using EnrichedHeatmap for visualization of NGS experiments
heatmap
chip-seq
atac-seq
EnrichedHeatmap
updated 13 months ago by
Ram
43k • written 4.7 years ago by
ATpoint
82k
15
votes
4
replies
4.6k
views
Tutorial:
RNASeq tutorial for gene differential expression analysis
Transcriptomics
bioconductor
RNA-Seq
R
updated 13 months ago by
Ram
43k • written 3.8 years ago by
Thind amarinder
▴ 340
26
votes
0
replies
2.5k
views
Tutorial:
Resources / databases for clinical interpretation of cancer variants
interpretation
cancer
annotation
variant
updated 13 months ago by
Ram
43k • written 4.6 years ago by
Malachi Griffith
19k
10
votes
1
reply
2.3k
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 13 months ago by
Ram
43k • written 4.1 years ago by
chen
★ 2.5k
60
votes
52
replies
44k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 13 months ago by
Ram
43k • written 7.6 years ago by
steve
★ 3.5k
13
votes
7
replies
6.2k
views
Tutorial:
STARsolo config for 10x Chromium v1, v2, v3
Chromium
10x
STARsolo
STAR
updated 13 months ago by
Ram
43k • written 3.6 years ago by
Kevin Blighe
87k
21
votes
26
replies
9.7k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 7 weeks ago by
Yao
▴ 30 • written 4.4 years ago by
Juke34
8.6k
0
votes
0
replies
1.1k
views
Tutorial:
BrainArray CDF, annotation, etc
db
brainarray
cdf
updated 13 months ago by
Ram
43k • written 3.6 years ago by
Kevin Blighe
87k
12
votes
0
replies
2.7k
views
Tutorial:
Long versus wide data for plotting genomics data in R.
ggplot2
tidyverse
data.table
R
updated 13 months ago by
Ram
43k • written 3.7 years ago by
rpolicastro
13k
1
vote
1
reply
1.4k
views
Tutorial:
Downloading GnuWin and using to convert txt to bed file for windows users
bed
bed2txt
sequencing
txt
updated 13 months ago by
Ram
43k • written 3.7 years ago by
opheevallee
• 0
4
votes
3
replies
4.6k
views
Tutorial:
How to get full taxonomy classification using taxize and myTAI
taxonomy
R
updated 13 months ago by
Ram
43k • written 6.1 years ago by
Daniel
★ 4.0k
4
votes
1
reply
1.4k
views
Tutorial:
Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
BED
BEDtools
updated 13 months ago by
Ram
43k • written 3.7 years ago by
sdsubaru33
▴ 40
3
votes
0
replies
3.7k
views
Tutorial:
Sorting GFF/GTF files
gtf
gff
updated 14 months ago by
Ram
43k • written 3.8 years ago by
Juke34
8.6k
20
votes
6
replies
5.6k
views
Tutorial:
Open Targets and programmatic access
open-targets
disease
API
drug
updated 13 months ago by
Ram
43k • written 7.6 years ago by
Denise CS
★ 5.2k
2
votes
2
replies
2.1k
views
Tutorial:
Human mitochondrial DNA annotation in SnpEff
chrMT
SNP
snpEff
updated 13 months ago by
Ram
43k • written 3.9 years ago by
Arup Ghosh
3.2k
12
votes
5
replies
2.5k
views
Tutorial:
FASTA file split
fasta
updated 13 months ago by
Ram
43k • written 3.9 years ago by
Juke34
8.6k
0
votes
0
replies
1.8k
views
Tutorial:
VIDEO: Installing BLAST Databases on Your Own Computer
BLAST-databases
Linux
sequence
MacOSX
updated 13 months ago by
Ram
43k • written 3.9 years ago by
brian.fristensky
▴ 460
0
votes
0
replies
1.0k
views
Tutorial:
VIDEO: BLAST Searches Through a Data Science Lens
Covid19
Data-Science
sequence
BLAST
updated 13 months ago by
Ram
43k • written 3.9 years ago by
brian.fristensky
▴ 460
2
votes
1
reply
1.6k
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 13 months ago by
Ram
43k • written 3.9 years ago by
chen
★ 2.5k
73
votes
27
replies
28k
views
16 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 5 months ago by
snardeli
• 0 • written 10.2 years ago by
Istvan Albert
100k
59
votes
43
replies
21k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 13 months ago by
Ram
43k • written 6.6 years ago by
Rox
★ 1.4k
20
votes
7
replies
6.4k
views
Tutorial:
Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2
RNA-Seq
R
updated 13 months ago by
Ram
43k • written 5.6 years ago by
ahmad mousavi
▴ 800
4
votes
0
replies
1.8k
views
Tutorial:
NIH CDE browser for TCGA clinical data CDE codes
nih
tcga
metadata
cde
updated 13 months ago by
Ram
43k • written 4.1 years ago by
Kevin Blighe
87k
10
votes
4
replies
11k
views
Tutorial:
Using the MinION MinKNOW software on Ubuntu 1604
long-reads
oxford-nanopore
minion
updated 13 months ago by
Ram
43k • written 4.8 years ago by
colindaven
6.4k
0
votes
0
replies
1.3k
views
Tutorial:
Training GeneMark-EP+ ab-initio tool
abinitio
training
genemark
annotation
updated 13 months ago by
Ram
43k • written 4.2 years ago by
Juke34
8.6k
2
votes
1
reply
3.2k
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 13 months ago by
Ram
43k • written 4.2 years ago by
Asad Prodhan
▴ 10
5
votes
0
replies
3.3k
views
Tutorial:
How to run CWL with Nextflow
cwl
nextflow
updated 13 months ago by
Ram
43k • written 4.2 years ago by
steve
★ 3.5k
5
votes
2
replies
2.3k
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 13 months ago by
Ram
43k • written 5.3 years ago by
linuxborg2
▴ 10
50
votes
3
replies
4.8k
views
Tutorial:
[[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 13 months ago by
Ram
43k • written 5.3 years ago by
ATpoint
82k
21
votes
9
replies
6.5k
views
8 follow
Tutorial:
Interactive Perl Learning
perl
updated 14 months ago by
Ram
43k • written 10.9 years ago by
Medhat
9.7k
288
votes
39
replies
183k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 13 months ago by
Ram
43k • written 9.7 years ago by
Obi Griffith
20k
64
votes
26
replies
14k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 13 months ago by
Ram
43k • written 6.6 years ago by
Kevin Blighe
87k
34
votes
15
replies
6.5k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 13 months ago by
Ram
43k • written 4.9 years ago by
Shicheng Guo
★ 9.4k
20
votes
4
replies
2.7k
views
Tutorial:
Bash One-liners collection on Github
bash
linux
shell
updated 13 months ago by
Ram
43k • written 5.0 years ago by
nim.1111.ou
▴ 180
15
votes
7
replies
6.4k
views
Tutorial:
Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq
peaks
R
HOMER
updated 13 months ago by
Ram
43k • written 8.0 years ago by
steve
★ 3.5k
2
votes
0
replies
4.7k
views
Tutorial:
Calculation of TSS Scores for ATAC-seq Data
next-gen-sequencing
updated 13 months ago by
Ram
43k • written 4.8 years ago by
Sael
▴ 20
0
votes
0
replies
1.1k
views
Tutorial:
Apply ALoFT to identify loss-of-function somatic or germline variants
ALoFT
updated 13 months ago by
Ram
43k • written 4.9 years ago by
Shicheng Guo
★ 9.4k
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 13 months ago by
Ram
43k • written 7.5 years ago by
TriS
★ 4.7k
10
votes
5
replies
24k
views
Tutorial:
Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 13 months ago by
Ram
43k • written 5.8 years ago by
Shicheng Guo
★ 9.4k
6
votes
3
replies
4.5k
views
Tutorial:
Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment
sequencing
RNA-seq
gene
updated 13 months ago by
Ram
43k • written 5.5 years ago by
contact
▴ 40
0
votes
0
replies
1.1k
views
Tutorial:
Introduction to Gen3 Webinar
gen3
open-source
data-commons
big-data
updated 13 months ago by
Ram
43k • written 5.2 years ago by
Danielle
▴ 310
0
votes
1
reply
1.4k
views
Tutorial:
SFA (Stochastic Frontier Analysis) Frontier 4.1
r
spss
updated 13 months ago by
Ram
43k • written 6.2 years ago by
helgasaraswati
▴ 10
4
votes
2
replies
3.6k
views
Tutorial:
Introduce OpenGene: an open source library for processing NGS data
NGS
sequencing
Julia
OpenGene
updated 13 months ago by
Ram
43k • written 8.2 years ago by
chen
★ 2.5k
29
votes
4
replies
4.5k
views
Tutorial:
Modern Statistics for Modern Biology
statistics
updated 13 months ago by
Ram
43k • written 5.3 years ago by
Jean-Karim Heriche
27k
411 results • Page
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Recent Votes
Comment: No INFO/info value in headers
how to combine multiple RNAseq count files into a single dataframe in R and unix
Comment: Greatly speed up conda by using mamba
Greatly speed up conda by using mamba
Comment: Converting CRAM to FastQ
Parametric or non-parametric tests for qPCR significance testing between treatments?
Answer: Converting CRAM to FastQ
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Answer: visualize GSEA
by
bk11
★ 2.4k
I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R
by
Erina
• 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
swbarnes2
14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
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Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file
by
GenoMax
142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme
by
e.r.zakiev
▴ 210
obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Understood Thank you!
Comment: Converting CRAM to FastQ
by
GenoMax
142k
You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Okay, that shows us the problem, but not what we need to solve it. But, for instance, are you sure that period after the sample name shou…
Comment: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1]. [1]: https://groups.goo…
Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In Plink, A1 is usually a minor allele and A2 a major allele. .frq (basic allele frequency report) Produced by --freq. …
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