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412 results • Page
2 of 9
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Votes
Replies
76
votes
14
replies
16k
views
15 follow
Tutorial:
List Of Bioinformatics Books
books
updated 15 months ago by
Ram
43k • written 11.0 years ago by
Medhat
9.7k
20
votes
14
replies
4.1k
views
Tutorial:
Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq
visualization
Windows
EaSeq
updated 13 months ago by
Ram
43k • written 8.0 years ago by
Mads Lerdrup
▴ 460
9
votes
14
replies
3.8k
views
6 follow
Tutorial:
Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 19 months ago by
Angelina_G
▴ 10 • written 2.2 years ago by
thehung92phuyen
▴ 40
30
votes
14
replies
16k
views
8 follow
Tutorial:
Installation of the MuSiC suite on unsupported Linux distributions
genome-music
linux
smg
updated 15 months ago by
Ram
43k • written 11.3 years ago by
Cyriac Kandoth
6.1k
55
votes
14
replies
93k
views
10 follow
Tutorial:
Using R in Conda
R
updated 14 months ago by
Ram
43k • written 3.8 years ago by
rohitsatyam102
▴ 870
64
votes
13
replies
13k
views
11 follow
Tutorial:
Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect
GATK
Picard
Exome
updated 2.3 years ago by
Ram
43k • written 9.5 years ago by
Chirag Nepal
★ 2.4k
46
votes
13
replies
15k
views
13 follow
Tutorial:
Methylation Analysis Tutorial in R - Part 1
R
cancer
methylation
updated 9 weeks ago by
Konstantinos
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
35
votes
13
replies
14k
views
9 follow
Tutorial:
How to get FASTQ reads from the Short Read Archive (SRA)
fastq
sra
updated 2.3 years ago by
liorglic
★ 1.4k • written 2.6 years ago by
Istvan Albert
100k
77
votes
13
replies
16k
views
12 follow
Tutorial:
Exploring cancer mutation data portals
TCGA
Cancer
ICGC
Data-Portal
Mutation
updated 2.6 years ago by
Ram
43k • written 10.0 years ago by
Malachi Griffith
20k
75
votes
13
replies
67k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r
cancer
classification
updated 18 months ago by
Ram
43k • written 10.5 years ago by
Nicholas Spies
★ 1.2k
18
votes
13
replies
2.2k
views
Tutorial:
Screen shots of text (please don't)!
meta
updated 12 months ago by
Ram
43k • written 7.1 years ago by
Michael
54k
7
votes
13
replies
13k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
bcftools
updated 11 months ago by
Ram
43k • written 5.3 years ago by
jaybee
▴ 170
21
votes
13
replies
11k
views
10 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
ascp
aspera
updated 6 months ago by
jude
• 0 • written 23 months ago by
ATpoint
82k
5
votes
13
replies
2.0k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 29 days ago by
ATpoint
82k • written 4 weeks ago by
BioinfGuru
★ 1.7k
8
votes
12
replies
6.8k
views
Tutorial:
Create your own VPN to access work resources from home
tinyproxy
OpenVPN
VPN
updated 13 months ago by
Ram
43k • written 8.0 years ago by
John
13k
34
votes
12
replies
30k
views
7 follow
Tutorial:
So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control
fastqc
updated 14 months ago by
Ram
43k • written 10.6 years ago by
Istvan Albert
100k
6
votes
11
replies
5.7k
views
6 follow
Tutorial:
Add count numbers to headers in a fasta file
genome
updated 15 months ago by
Ram
43k • written 7.4 years ago by
wu.zhiqiang.1020
▴ 50
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
14 months ago by
Ram
43k
12
votes
11
replies
7.6k
views
Tutorial:
How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI
Bioproject
SRA
BioSample
updated 12 months ago by
Ram
43k • written 7.2 years ago by
CandiceChuDVM
★ 2.4k
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 14 months ago by
Ram
43k • written 7.6 years ago by
TriS
★ 4.7k
6
votes
10
replies
5.3k
views
Tutorial:
Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR
dna-methylation
updated 14 months ago by
Ram
43k • written 6.2 years ago by
dec986
▴ 380
30
votes
10
replies
83k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 14 months ago by
Ram
43k • written 3.2 years ago by
Nitin Narwade
★ 1.6k
22
votes
10
replies
7.1k
views
Tutorial:
Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse
gene
R
updated 14 months ago by
Ram
43k • written 3.7 years ago by
rpolicastro
13k
9
votes
9
replies
4.2k
views
Tutorial:
Determine % of reference genome covered by aligned SAM/BAM
reference-coverage
ngs
updated 12 months ago by
Ram
43k • written 6.7 years ago by
Kevin Blighe
88k
16
votes
9
replies
7.2k
views
Tutorial:
TCGA transcriptome data to R (DESeq2)
TCGA
GDC
DESeq2
updated 23 months ago by
dk0319
▴ 70 • written 2.5 years ago by
Barry Digby
★ 1.3k
21
votes
9
replies
6.6k
views
8 follow
Tutorial:
Interactive Perl Learning
perl
updated 14 months ago by
Ram
43k • written 10.9 years ago by
Medhat
9.7k
8
votes
9
replies
11k
views
Tutorial:
Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq
fasta
updated 14 months ago by
Ram
43k • written 10.1 years ago by
umer.zeeshan.ijaz
★ 1.8k
40
votes
9
replies
11k
views
10 follow
Tutorial:
Resources for flow cytometry bioinformatics
single-cell
flow-cytometry
updated 14 months ago by
Ram
43k • written 10.1 years ago by
Ahill
★ 1.9k
66
votes
9
replies
49k
views
7 follow
Tutorial:
Reference Assembly - Mapping Reads To A Reference Genome
reference
samtools
mapping
bwa
updated 15 months ago by
Ram
43k • written 10.9 years ago by
Joseph Hughes
★ 3.0k
7
votes
8
replies
3.4k
views
Tutorial:
Determine if a transcription factor is bound with CENTIPEDE
ChIP-Seq
transcription-factor
DNase-Seq
CENTIPEDE
updated 17 months ago by
Ram
43k • written 8.9 years ago by
Kamil
★ 2.3k
81
votes
8
replies
8.6k
views
6 follow
Tutorial:
Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop
lectures
genomics
training
updated 14 months ago by
Ram
43k • written 9.9 years ago by
Malachi Griffith
20k
23
votes
8
replies
5.4k
views
Tutorial:
A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K
methylation
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
brentp
24k
31
votes
8
replies
11k
views
7 follow
Tutorial:
How To Create A Bioinformatics Pipeline Using Spotify !
python
pipeline
updated 14 months ago by
Ram
43k • written 10.1 years ago by
Rad
▴ 810
99
votes
8
replies
29k
views
8 follow
Tutorial:
Guide to TCGA data
cancer
RNA-Seq
clinical
TCGA
updated 13 months ago by
Ram
43k • written 8.2 years ago by
Jordan Anaya
★ 1.1k
19
votes
7
replies
6.7k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count
scRNA-seq
RNA-Seq
updated 10 months ago by
ATpoint
82k • written 4.2 years ago by
colindaven
6.4k
15
votes
7
replies
6.5k
views
Tutorial:
Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq
peaks
R
HOMER
updated 14 months ago by
Ram
43k • written 8.0 years ago by
steve
★ 3.5k
12
votes
7
replies
2.3k
views
Tutorial:
Sequence Alignment from Scratch with BWA
alignment
bwa
DNA
13 months ago by
barslmn
★ 2.2k
13
votes
7
replies
6.3k
views
Tutorial:
STARsolo config for 10x Chromium v1, v2, v3
Chromium
10x
STARsolo
STAR
updated 14 months ago by
Ram
43k • written 3.7 years ago by
Kevin Blighe
88k
8
votes
7
replies
8.4k
views
Tutorial:
Getting Cegma/Genewise To Work On Centos, Rhel
centos
genewise
rhel
cegma
updated 2.3 years ago by
Ram
43k • written 10.5 years ago by
Adrian Pelin
★ 2.6k
16
votes
7
replies
16k
views
Tutorial:
Integrating VDJ sequencing data with Seurat
VDJ
Seurat
sc-RNAseq
clonotyping
updated 14 months ago by
Ram
43k • written 4.9 years ago by
atakanekiz
▴ 310
50
votes
7
replies
11k
views
7 follow
Tutorial:
Genome Assembly Review Papers
assembly
papers
updated 15 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
11
votes
7
replies
14k
views
Tutorial:
Removing rows with duplicate values based on 1 or more key values - linux awk
awk
linux
bash
updated 12 months ago by
Ram
43k • written 6.7 years ago by
Kevin Blighe
88k
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 14 months ago by
Ram
43k • written 5.6 years ago by
ahmad mousavi
▴ 800
11
votes
7
replies
12k
views
Tutorial:
ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler
Software
rna-seq
updated 12 months ago by
Ram
43k • written 3.2 years ago by
Novogene
▴ 420
16
votes
6
replies
6.5k
views
Tutorial:
How to make your snakefiles self-documenting
snakemake
updated 13 months ago by
Ram
43k • written 7.5 years ago by
Botond Sipos
★ 1.7k
13
votes
6
replies
6.0k
views
Tutorial:
Trim & align paired-end reads in a single pass
align
trim
fastq
pipe
paired-end
updated 13 months ago by
Ram
43k • written 7.9 years ago by
dariober
14k
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
6.1k
30
votes
6
replies
22k
views
Tutorial:
Transforming And Manipulating Color Space Reads
conversion
solid
updated 20 months ago by
Ram
43k • written 12.1 years ago by
Istvan Albert
100k
61
votes
6
replies
9.5k
views
Tutorial:
Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 14 months ago by
Ram
43k • written 10.8 years ago by
Medhat
9.7k
106
votes
6
replies
26k
views
6 follow
Tutorial:
Creating workflows with snakemake and conda
workflow
snakemake
conda
updated 14 months ago by
Ram
43k • written 5.7 years ago by
finswimmer
16k
412 results • Page
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Recent Replies
Comment: GO analysis: Indicate genes corresponding to the pathway
by
marco.barr
▴ 130
I think you have set a filter to get these pahways upstream from the DEG results. You should extract the IDs or names of the genes that you…
Comment: GATK Structural Variants Pipeline - Steps
by
Bioinformatics_begginner
▴ 20
Thank you for the response, I mean those tools aren't all the steps from fasta to vcf. Would be key understanding the aligner, reference us…
Comment: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
GenoMax
142k
Please accept the answer (green check mark) to provide closure to this thread.
Answer: GATK Structural Variants Pipeline - Steps
by
Pierre Lindenbaum
161k
> A structural variation pipeline for short-read sequencing https://github.com/broadinstitute/gatk-sv
Comment: GATK Structural Variants Pipeline - Steps
by
DGTool
▴ 20
If it is just the tools that they used which you are looking for, the first link in the overview section of that page leads to the followin…
Comment: GO analysis: p-value range
by
Matthias Zepper
4.6k
It is just a warning that you add a new scale to a ggplot2 plot, that already has an existing one, which will get replaced. Nothing to worr…
Comment: GO analysis: p-value range
by
marco.barr
▴ 130
If you write me the code you used I can help you more
Comment: GO analysis: p-value range
by
sooni
▴ 20
When I run the code, the following message appears: Scale for y is already present. Adding another scale for y, which will replace…
Comment: Why most genes have high padj values
by
mnx0723
• 0
In the case of other samples, the total number of genes is at least 3,000 more than that one, but it seems to be a relatively small number.…
Comment: How to hide label in layout file of MCscan (python version)
by
jinyi
• 0
Command line is as follows: python -m jcvi.graphics.synteny Cs.Cm.i1.blocks Cs_Cm.bed layout2.txt
Comment: Add stats to the plot
by
marco.barr
▴ 130
Thank you, it seems to be clearer. Your Condition already has two factorial levels. You can replace these names in groups 1 and 2. da…
Comment: Error in using BioSampleParser tool: subscript out of bounds
by
marco.barr
▴ 130
Hi, I also had the same problem. If you check its github page there have been no releases for many years and these errors cannot be fixed. …
Comment: Add stats to the plot
by
Ghada
• 0
Thanks, thats really helpful ![enter image description here][1] ![enter image description here][2] [1]: /media/images/0470f3dc-5945-…
Comment: PCA Visualization error in R
by
marco.barr
▴ 130
SNPRelate is an R package that is able to read from VCF files directly and perform PCA and IBD/IBS. See the documentation for details in Bi…
Comment: Why most genes have high padj values
by
ATpoint
82k
788 differential genes is a lot. What is the problem?
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