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141 results • Page
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239
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176
replies
95k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 11 months ago by
Ram
43k • written 8.7 years ago by
TriS
★ 4.7k
98
votes
106
replies
46k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 11 days ago by
psb7
▴ 20 • written 5.6 years ago by
Kevin Blighe
87k
149
votes
70
replies
50k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 7 months ago by
Raheleh
▴ 260 • written 6.4 years ago by
Kevin Blighe
87k
90
votes
48
replies
33k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 5 months ago by
Ram
43k • written 10.5 years ago by
Irsan
★ 7.8k
83
votes
34
replies
19k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 10 months ago by
adelheidkratzer
• 0 • written 5.8 years ago by
egeulgen
★ 1.3k
10
votes
31
replies
11k
views
10 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 5 months ago by
ha2606
• 0 • written 6.3 years ago by
vimalkvn
▴ 320
49
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 22 days ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 5 weeks ago by
jkbonfield
★ 1.2k • written 5.1 years ago by
finswimmer
16k
84
votes
29
replies
32k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 9 months ago by
amziepickles
• 0 • written 8.1 years ago by
Obi Griffith
20k
73
votes
27
replies
28k
views
16 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 4 months ago by
snardeli
• 0 • written 10.2 years ago by
Istvan Albert
100k
21
votes
26
replies
9.6k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 5 weeks ago by
Yao
▴ 30 • written 4.4 years ago by
Juke34
8.5k
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 1 day ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
93
votes
23
replies
91k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 3 months ago by
clara.apicella
• 0 • written 5.7 years ago by
otwtgin2010
▴ 610
35
votes
17
replies
16k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning
classification
updated 11 months ago by
GenoMax
141k • written 10.4 years ago by
Obi Griffith
20k
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 4 weeks ago by
aUser
▴ 30 • written 7.5 years ago by
martinguerrerog89
▴ 310
39
votes
16
replies
36k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 3 months ago by
GenoMax
141k • written 3.7 years ago by
lavinia.gordon
▴ 160
65
votes
15
replies
14k
views
Tutorial:
Which human reference genome should I use?
assembly
genome
alignment
updated 11 months ago by
Ram
43k • written 5.5 years ago by
finswimmer
16k
21
votes
13
replies
10k
views
10 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
ascp
aspera
updated 5 months ago by
jude
• 0 • written 22 months ago by
ATpoint
81k
7
votes
13
replies
13k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
bcftools
updated 10 months ago by
Ram
43k • written 5.2 years ago by
jaybee
▴ 170
46
votes
13
replies
15k
views
13 follow
Tutorial:
Methylation Analysis Tutorial in R - Part 1
R
cancer
methylation
updated 5 weeks ago by
Konstantinos
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
18
votes
13
replies
2.2k
views
Tutorial:
Screen shots of text (please don't)!
meta
updated 11 months ago by
Ram
43k • written 7.1 years ago by
Michael
54k
12
votes
11
replies
7.5k
views
Tutorial:
How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI
Bioproject
SRA
BioSample
updated 11 months ago by
Ram
43k • written 7.1 years ago by
CandiceChuDVM
★ 2.4k
4
votes
10
replies
575
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
1 hour ago by
BioinfGuru
★ 1.7k
9
votes
9
replies
4.2k
views
Tutorial:
Determine % of reference genome covered by aligned SAM/BAM
reference-coverage
ngs
updated 11 months ago by
Ram
43k • written 6.6 years ago by
Kevin Blighe
87k
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 11 months ago by
Ram
43k • written 6.6 years ago by
Kevin Blighe
87k
19
votes
7
replies
6.5k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count
scRNA-seq
RNA-Seq
updated 9 months ago by
ATpoint
81k • written 4.1 years ago by
colindaven
6.3k
11
votes
7
replies
11k
views
Tutorial:
ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler
Software
rna-seq
updated 11 months ago by
Ram
43k • written 3.1 years ago by
Novogene
▴ 420
39
votes
6
replies
19k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 11 months ago by
Ram
43k • written 6.6 years ago by
steve
★ 3.5k
10
votes
6
replies
4.1k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 24 days ago by
Ram
43k • written 6.2 years ago by
Kevin Blighe
87k
1
vote
5
replies
596
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq
TOSICA
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
37
votes
5
replies
6.1k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 7 months ago by
gallardodiazmiriam
▴ 20 • written 8.8 years ago by
Luke Crichton
▴ 430
9
votes
5
replies
2.3k
views
Tutorial:
What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 11 months ago by
Ram
43k • written 6.8 years ago by
Istvan Albert
100k
5
votes
5
replies
6.9k
views
Tutorial:
use firehose_get to download TCGA data
tcga
RNA-Seq
updated 11 months ago by
Ram
43k • written 6.4 years ago by
jmzeng1314
▴ 130
0
votes
4
replies
715
views
Tutorial:
Reverse pharmacology: how to predict drugs with genes or disease names?
drugs
drug-targets
genes
5 months ago by
Coremine Medical
▴ 20
9
votes
4
replies
5.5k
views
Tutorial:
Unsupervised clustering on gene expression data
gene-expression
clustering
RNA-seq
8 months ago by
Hamid Ghaedi
3.2k
1
vote
4
replies
3.3k
views
Tutorial:
Applying machine learning to NGS transcriptomic data
next-gen
RNA-Seq
updated 11 months ago by
Ram
43k • written 5.9 years ago by
elia.brodsky
▴ 340
3
votes
4
replies
4.5k
views
Tutorial:
gencore: a tool to reduce sequencing noises by generating consensus reads
consensus
OpenGene
sequencing-noise
updated 11 months ago by
Ram
43k • written 6.0 years ago by
chen
★ 2.5k
3
votes
4
replies
3.6k
views
Tutorial:
Gene Set Enrichment Analysis on T-BioInfo
gene
RNA-Seq
updated 11 months ago by
Ram
43k • written 5.5 years ago by
elia.brodsky
▴ 340
2
votes
3
replies
2.7k
views
Tutorial:
It's about the journey, and not the destination
R
network
updated 11 months ago by
Ram
43k • written 7.0 years ago by
theobroma22
★ 1.2k
7
votes
3
replies
2.7k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 17 hours ago by
colindaven
6.3k • written 15 months ago by
Dr.Animo
▴ 130
3
votes
3
replies
1.1k
views
Tutorial:
multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation
RNAseq
multiomics
updated 3 months ago by
sil_bioinfo
▴ 40 • written 7 months ago by
Ming Tommy Tang
★ 3.9k
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 8 months ago by
William
▴ 30 • written 7.0 years ago by
kirannbishwa01
★ 1.6k
3
votes
3
replies
8.8k
views
Tutorial:
High Speed Downloading of SRA, SAM and Fastq Files
fastq
sam
Aspera-Connect
sra
updated 11 months ago by
Ram
43k • written 6.3 years ago by
Wenhu_Cao
▴ 100
2
votes
3
replies
539
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis with DEseq2
python
pyDESeq2
RNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
6
votes
2
replies
5.0k
views
Tutorial:
Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
4 months ago by
GenoMax
141k
7
votes
2
replies
1.9k
views
Tutorial:
Introduction to Human Genomics for Clinical Informaticists
genome
updated 11 months ago by
Ram
43k • written 6.7 years ago by
bdolin
▴ 90
1
vote
2
replies
1.5k
views
Tutorial:
ViennaRNA package installation in Windows
windows
rna
mfold
viennarna
updated 10 months ago by
Ram
43k • written 19 months ago by
Sandhiya
▴ 20
5
votes
2
replies
3.1k
views
Tutorial:
Get GC Content from UCSC with perl script (mysql)
myql
ucsc
gc-content
perl
updated 11 months ago by
Ram
43k • written 7.0 years ago by
Shicheng Guo
★ 9.4k
3
votes
2
replies
2.6k
views
Tutorial:
Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences
Workshops
updated 11 months ago by
Ram
43k • written 7.0 years ago by
jnowacki
▴ 100
1
vote
2
replies
867
views
Tutorial:
How to ask computational biology questions
computational-biology
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
141 results • Page
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bcftools multiple commands
bcftools pipe generated file from first command with second
C: How to setup a Summarized Experiment
A: How to download genome assemblies from NCBI with a list of GCA identifiers?
what's the genomic location and name of gene responsible for orange and black patches in calico cats
Comment: featureCounts --primary tag counting uniquely mapped reads and excludes multi-ma
Answer: Duplicate marking, read names, and the SRA
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Answer: MEGA Analysis Issue on High-Performance Computer
by
Mensur Dlakic
★ 27k
> I have ensured that I am using the latest version of MEGA and that other applications are not consuming excessive resources during the an…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Some of us are still learning and fall foul to knowledge limitation fairly regularly. Luckily we have people to put us in our place.
Answer: Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
by
GenoMax
141k
> I know that I should be able to collect protein sequences from the blastp results into a file, but I do not know how to do this. You c…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
rheab1230
▴ 140
I got the normalized gene count from gtex portal. they use inverse quantile normalization
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
Matthias Zepper
4.5k
It is not entirely off, but evidently also not correct. Melanin biosynthesis is a multistep process, that indeed prominently involves the…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
> so a single Rscript could utilise multiple environments and versions How is that sane, let alone "better"? Also, why use `snap` for curl…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
Ram
43k
Normalized how?
Comment: Duplicate marking, read names, and the SRA
by
GenoMax
141k
With public data one has to work with what is there. If the information about position is absent then only thing that could be done is to l…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Or better yet. To have an R package that allows access to conda environments via "conda list env" so that environments can be switched with…
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
GenoMax
141k
If GPT is right then it says that: > The specific gene responsible for the orange and non-orange (black or > gray) fur colors in cats is t…
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
Jean-Karim Heriche
27k
As far as I know the Orange locus hasn't been mapped to a gene. Maybe this paper will help in narrowing the search: https://www.ncbi.nlm.ni…
Comment: Duplicate marking, read names, and the SRA
by
Luka
• 0
>Curios if there a reference for this? [Apparently it's not deprecated yet][1], but will be soon and the SRA intends for it to be at some …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
I prefer RStudio for new projects as well. The moment I need versions though, RStudio becomes a burden. I wish one could launch RStudio fro…
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
GenoMax
141k
According to ChatGPT: The gene responsible for the orange and black patches of fur in calico cats (and tortoiseshell cats) is the X-linked …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Certainly true. Switching versions is way simpler that way, at the cost of the familiarity of the Rstudio IDE - especially if the code is w…
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