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412 results • Page
3 of 9
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Votes
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20
votes
4
replies
8.6k
views
Tutorial:
DE analysis by edgeR
RNA-Seq
R
edgeR
updated 13 months ago by
Ram
44k • written 7.7 years ago by
zizigolu
★ 4.3k
20
votes
2
replies
8.1k
views
Tutorial:
Creating a karyotype plot with genes using karyoploteR
karyoploteR
visualization
R
genome
updated 12 months ago by
Ram
44k • written 6.5 years ago by
bernatgel
★ 3.4k
20
votes
2
replies
3.4k
views
Tutorial:
Beginner's Handbook to Next Generation Sequencing
NGS
updated 12 months ago by
Ram
44k • written 7.1 years ago by
support
▴ 650
19
votes
3
replies
14k
views
Tutorial:
bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 22 months ago by
Ram
44k • written 8.3 years ago by
Shicheng Guo
★ 9.4k
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
19
votes
4
replies
8.9k
views
Tutorial:
Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 15 months ago by
Ram
44k • written 11.2 years ago by
Istvan Albert
100k
18
votes
2
replies
10k
views
Tutorial:
Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq
Galaxy
IGB
updated 2.2 years ago by
Ram
44k • written 9.6 years ago by
Nowlan Freese
▴ 860
18
votes
2
replies
5.9k
views
Tutorial:
Update kraken databases
database
kraken
k-mer
python
updated 12 months ago by
Ram
44k • written 7.1 years ago by
Sej Modha
5.3k
18
votes
40
replies
19k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 3.9 years ago by
krishdb38
• 0 • written 7.9 years ago by
Esaie
▴ 170
18
votes
13
replies
2.2k
views
Tutorial:
Screen shots of text (please don't)!
meta
updated 12 months ago by
Ram
44k • written 7.2 years ago by
Michael
54k
17
votes
0
replies
6.6k
views
Tutorial:
Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course
training
updated 15 months ago by
Ram
44k • written 11.9 years ago by
Istvan Albert
100k
17
votes
0
replies
13k
views
Tutorial:
Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 15 months ago by
Ram
44k • written 12.1 years ago by
David Langenberger
11k
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
44k • written 7.6 years ago by
TriS
★ 4.7k
16
votes
5
replies
13k
views
6 follow
Tutorial:
Easy way to do GO enrichment in R
enrichr
RNA-Seq
gene
R
updated 14 months ago by
Ram
44k • written 6.5 years ago by
ahmad mousavi
▴ 800
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
16
votes
5
replies
9.0k
views
Tutorial:
Using The Biomart Perl Api For Simple Queries
api
perl
biomart
updated 15 months ago by
Ram
44k • written 11.7 years ago by
Obi Griffith
20k
16
votes
6
replies
6.5k
views
Tutorial:
How to make your snakefiles self-documenting
snakemake
updated 13 months ago by
Ram
44k • written 7.6 years ago by
Botond Sipos
★ 1.7k
16
votes
3
replies
4.7k
views
Tutorial:
NCBI blast tutorial
ncbi
blast
updated 13 months ago by
Ram
44k • written 8.1 years ago by
Eric Normandeau
11k
16
votes
3
replies
4.5k
views
Tutorial:
Methylation Analysis Tutorial in R_part2
cancer
methylation
RNA-Seq
R
updated 3.2 years ago by
zhuanggj706
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
16
votes
7
replies
16k
views
Tutorial:
Integrating VDJ sequencing data with Seurat
VDJ
Seurat
sc-RNAseq
clonotyping
updated 14 months ago by
Ram
44k • written 4.9 years ago by
atakanekiz
▴ 310
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
44k
15
votes
2
replies
2.1k
views
Tutorial:
Germline variant calling pipeline using Snakemake
snakemake
GATK
germline_variant_calling
updated 19 months ago by
brunobsouzaa
▴ 830 • written 2.7 years ago by
nhaus
▴ 360
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
44k • written 8.0 years ago by
steve
★ 3.5k
15
votes
1
reply
4.0k
views
Tutorial:
Dealing with nanopore fast5 files compressed with vbz
hdf5
nanopore
fast5
vbz
MinKNOW
updated 20 months ago by
Assa Yeroslaviz
★ 1.8k • written 2.4 years ago by
dariober
14k
15
votes
1
reply
3.2k
views
Tutorial:
Current Topics in Genome Analysis 2016 (collection of educational lectures)
genomics
training
lectures
workshop
updated 13 months ago by
Ram
44k • written 8.0 years ago by
Malachi Griffith
20k
15
votes
5
replies
16k
views
Tutorial:
How to create a mutation lolliplot with GenVisR
bioconductor
graphics
R
genvisr
updated 13 months ago by
Ram
44k • written 7.9 years ago by
Obi Griffith
20k
15
votes
1
reply
7.2k
views
Tutorial:
A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl
SAM
blast
BED
updated 12 months ago by
Ram
44k • written 6.5 years ago by
Joseph Hughes
★ 3.0k
15
votes
2
replies
3.1k
views
Tutorial:
Introduction to bedtools.
bedtools
updated 14 months ago by
Ram
44k • written 9.5 years ago by
Aaronquinlan
12k
15
votes
4
replies
4.6k
views
Tutorial:
RNASeq tutorial for gene differential expression analysis
Transcriptomics
bioconductor
RNA-Seq
R
updated 14 months ago by
Ram
44k • written 3.8 years ago by
Thind amarinder
▴ 340
15
votes
2
replies
6.9k
views
Tutorial:
Genotype And Snp Calling Review Papers
snp
updated 15 months ago by
Ram
44k • written 11.7 years ago by
Istvan Albert
100k
14
votes
2
replies
6.5k
views
Tutorial:
ChIP-seq analysis tutorial
ChIP-Seq
updated 13 months ago by
Ram
44k • written 8.7 years ago by
Ming Tommy Tang
★ 3.9k
14
votes
2
replies
2.4k
views
Tutorial:
Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
SNP
R
updated 13 months ago by
Ram
44k • written 8.2 years ago by
Jeremy Leipzig
22k
14
votes
0
replies
8.4k
views
Tutorial:
Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
IGB
ChIP-Seq
Galaxy
MACS
RNA-Seq
updated 2.2 years ago by
Ram
44k • written 9.4 years ago by
Nowlan Freese
▴ 860
14
votes
3
replies
20k
views
Tutorial:
Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome
plot
coverage
samtools
updated 9 months ago by
William
▴ 30 • written 7.1 years ago by
kirannbishwa01
★ 1.6k
14
votes
31
replies
6.9k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
geneset
genome
gene
abinitio
updated 14 months ago by
Ram
44k • written 4.8 years ago by
Juke34
8.6k
14
votes
1
reply
3.1k
views
Tutorial:
PCR Primer or Primer+Probe design
pcr
probe
rt-pcr
qpcr
primer
updated 3.0 years ago by
jared.andrews07
★ 17k • written 3.0 years ago by
Kevin Blighe
88k
14
votes
0
replies
9.6k
views
Tutorial:
How to generate PCA plot and heatmaps in R
heatmap
PCA
RNA-Seq
R
updated 13 months ago by
Ram
44k • written 7.7 years ago by
Ming Tommy Tang
★ 3.9k
13
votes
3
replies
5.2k
views
Tutorial:
Video: Visualization of whole genome DNA methylation data in IGB
Bismark
BS-Seq
RNA-Seq
IGB
updated 2.0 years ago by
Ram
44k • written 9.2 years ago by
Nowlan Freese
▴ 860
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
44k • written 3.7 years ago by
Kevin Blighe
88k
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
44k • written 7.9 years ago by
dariober
14k
12
votes
0
replies
2.8k
views
Tutorial:
Long versus wide data for plotting genomics data in R.
ggplot2
tidyverse
data.table
R
updated 14 months ago by
Ram
44k • written 3.7 years ago by
rpolicastro
13k
12
votes
17
replies
3.0k
views
Tutorial:
How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola
bwa
updated 17 months ago by
Ram
44k • written 8.9 years ago by
Istvan Albert
100k
12
votes
1
reply
5.1k
views
Tutorial:
RepSeq data processing and analysis
immunology
tcr
repseq
sequencing
repertoire
updated 19 months ago by
Ram
44k • written 8.8 years ago by
mikhail.shugay
3.5k
12
votes
5
replies
2.5k
views
Tutorial:
FASTA file split
fasta
updated 14 months ago by
Ram
44k • written 3.9 years ago by
Juke34
8.6k
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
44k • written 7.2 years ago by
CandiceChuDVM
★ 2.5k
12
votes
6
replies
5.0k
views
Tutorial:
sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 22 months ago by
Ram
44k • written 8.3 years ago by
zizigolu
★ 4.3k
12
votes
7
replies
2.3k
views
Tutorial:
Sequence Alignment from Scratch with BWA
alignment
bwa
DNA
14 months ago by
barslmn
★ 2.2k
12
votes
5
replies
8.4k
views
Tutorial:
How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 13 months ago by
Ram
44k • written 8.0 years ago by
Shicheng Guo
★ 9.4k
12
votes
20
replies
14k
views
10 follow
Tutorial:
Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell
RNA-Seq
seurat
TCR
updated 14 months ago by
Ram
44k • written 5.0 years ago by
jared.andrews07
★ 17k
12
votes
4
replies
5.4k
views
Tutorial:
*FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux
R
updated 15 months ago by
Ram
44k • written 3.3 years ago by
garden_giessen
▴ 130
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A: Fold change - a final explanation
Comment: scRNA-seq quality control
Comment: How to get the ratio of allele counts from GATK derived VCF file?
Setting up Aspera Connect (ascp) on Linux and macOS
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Answer: Genes' fpkm values through cufflink
Answer: Genes' fpkm values through cufflink
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Comment: Is it possible to run CibersortX with a very small number of samples?
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▴ 330
Thanks. I have checked that all files are tab delimited, with the first column named Gene_Symbols, with capitalized gene symbols, and no qu…
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aw7
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Someone, presumably you, opened an [issue][1] for the same problem. The answer was: > This problem should be fixed in htslib 1.20 (incl…
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i.sudbery
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If you are asking StringTie to estimate expression, then you need to provide it with BAM or CRAM files of the original reads, not a stringt…
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emmanouil.a
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personaly I see the workstations in long-term ... maybe today you are running only scRNA but having a good workstation tomorrow you can als…
Comment: Z score
by
Akash D
▴ 40
Alright! Got you...
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
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i.sudbery
19k
It very much depends on whether the OP does want/need to do the CellRanger runs locally or not. Doesn't really matter if its only occasion…
Comment: log2 fold change in RNA-seq analysis
by
Mensur Dlakic
★ 27k
Everything is already explained on this page, just read everything already written above. Specifically, [**this comment**][1]. [1]: htt…
Comment: log2 fold change in RNA-seq analysis
by
May Ling
• 0
Good day everyone, Sorry I found a bit confusing and would appreciate if I could clarify on the calculation. I am using DESeq. My desire…
Answer: GWAS Phenotypes
by
韩雨
• 0
In my opinion, the basis of the question is to solve whether the phenotype is regulated by genetics. In the aspect of genetic, the estima…
Answer: Classic threshold for log2 fold change in RNA-seq experiment
by
May Ling
• 0
Good day everyone, Sorry I found a bit confusing and would appreciate if I could clarify on the calculation. I am using DESeq. My desire…
Comment: some error in building kraken2 database
by
ahmet
• 0
Were you able to fix this issue? I'm also trying to add external species to krakendb
Comment: Z score
by
ATpoint
82k
logFCs are a bit difficult to cluster I think, because fold changes without stats attached to it are meaningless. They can be very big, due…
Comment: Z score
by
Akash D
▴ 40
Ok. However, if i perform it on log2FC, there wont be any control samples visible in my heatmap. Your answer is perfect.
Comment: Z score
by
ATpoint
82k
You can apply Z-scores on whatever you want, but it must make sense and depends on what you want to do. What is the context? See for exampl…
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