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412 results • Page
2 of 9
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Votes
Replies
50
votes
1
reply
8.9k
views
Tutorial:
Basic normalization, batch correction and visualization of RNA-seq data
edger
RNA-seq
updated 15 months ago by
Ram
43k • written 3.7 years ago by
ATpoint
82k
50
votes
3
replies
4.8k
views
Tutorial:
[[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 14 months ago by
Ram
43k • written 5.3 years ago by
ATpoint
82k
50
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 7 weeks ago by
Istvan Albert
100k • written 8.2 years ago by
Ram
43k
47
votes
19
replies
14k
views
8 follow
Tutorial:
Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control
fastqc
updated 16 months ago by
Ram
43k • written 11.2 years ago by
Istvan Albert
100k
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
46
votes
6
replies
25k
views
Tutorial:
Greatly speed up conda by using mamba
software
updated 2.3 years ago by
cameron.cowan
▴ 50 • written 3.1 years ago by
rpolicastro
13k
45
votes
2
replies
37k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
updated 15 months ago by
Ram
43k • written 12.1 years ago by
MSU course 2011
▴ 540
45
votes
3
replies
13k
views
Tutorial:
A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics
computational-biology
updated 13 months ago by
Ram
43k • written 8.1 years ago by
Sinji
★ 3.2k
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
42
votes
2
replies
18k
views
Tutorial:
Sequencing Technology Review Papers
sequencing
papers
updated 14 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
42
votes
16
replies
24k
views
15 follow
Tutorial:
Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC
varscan2
CNV
copy-number
updated 21 months ago by
Ram
43k • written 8.7 years ago by
Chirag Nepal
★ 2.4k
42
votes
19
replies
7.9k
views
8 follow
Tutorial:
Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 14 months ago by
Ram
43k • written 11.2 years ago by
Daniel Standage
4.1k
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
39
votes
16
replies
37k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 4 months ago by
GenoMax
142k • written 3.8 years ago by
lavinia.gordon
▴ 160
39
votes
6
replies
20k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 12 months ago by
Ram
43k • written 6.7 years ago by
steve
★ 3.5k
37
votes
5
replies
6.1k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 8 months ago by
gallardodiazmiriam
▴ 20 • written 8.8 years ago by
Luke Crichton
▴ 430
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 12 months ago by
GenoMax
142k • written 10.5 years ago by
Obi Griffith
20k
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
34
votes
15
replies
6.5k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 14 months ago by
Ram
43k • written 4.9 years ago by
Shicheng Guo
★ 9.4k
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 8 weeks ago by
aUser
▴ 30 • written 7.6 years ago by
martinguerrerog89
▴ 310
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
32
votes
6
replies
12k
views
Tutorial:
A simple tutorial for a complex ComplexHeatmap
clustering
pam
arthritis
ComplexHeatmap
updated 14 months ago by
Ram
43k • written 4.0 years ago by
Kevin Blighe
88k
32
votes
4
replies
8.0k
views
Tutorial:
Fast LD computation from VCF files using tomahawk
ld
snp
vcf
vcftools
bcftools
updated 14 months ago by
Ram
43k • written 5.5 years ago by
firestar
★ 1.6k
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
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
30
votes
14
replies
16k
views
8 follow
Tutorial:
Installation of the MuSiC suite on unsupported Linux distributions
genome-music
linux
smg
updated 14 months ago by
Ram
43k • written 11.3 years ago by
Cyriac Kandoth
6.1k
30
votes
10
replies
82k
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
29
votes
5
replies
6.4k
views
Tutorial:
Gnu Parallel Tutorial
parallel
gnu-parallel
updated 14 months ago by
Ram
43k • written 10.7 years ago by
ole.tange
★ 4.4k
29
votes
4
replies
4.5k
views
Tutorial:
Modern Statistics for Modern Biology
statistics
updated 14 months ago by
Ram
43k • written 5.3 years ago by
Jean-Karim Heriche
27k
28
votes
0
replies
3.7k
views
Tutorial:
Building Docker images
singularity
docker
container
22 months ago by
ATpoint
82k
26
votes
0
replies
2.5k
views
Tutorial:
Resources / databases for clinical interpretation of cancer variants
interpretation
cancer
annotation
variant
updated 14 months ago by
Ram
43k • written 4.6 years ago by
Malachi Griffith
20k
26
votes
15
replies
8.9k
views
8 follow
Tutorial:
Syllabus To Learn Bioinformatics From Online Video Resources
course
training
mooc
updated 14 months ago by
Ram
43k • written 11.3 years ago by
Medhat
9.7k
26
votes
17
replies
7.8k
views
8 follow
Tutorial:
virtualenv - running Python based software in isolation
python
virtualenv
updated 20 months ago by
Ram
43k • written 9.8 years ago by
Ian
6.0k
24
votes
4
replies
7.7k
views
Tutorial:
Using EnrichedHeatmap for visualization of NGS experiments
heatmap
chip-seq
atac-seq
EnrichedHeatmap
updated 14 months ago by
Ram
43k • written 4.8 years ago by
ATpoint
82k
23
votes
19
replies
6.9k
views
10 follow
Tutorial:
MutScan: Detect important mutations by scanning FastQ files directly
fastq
mutation
cancer
target
updated 13 months ago by
Ram
43k • written 7.6 years ago by
chen
★ 2.5k
23
votes
2
replies
5.9k
views
Tutorial:
Extracting genomic feature sequences from GTF/GFF files with AGAT
extract
GTF
GFF
sequence
updated 20 months ago by
eggrandio
▴ 40 • written 3.1 years ago by
Juke34
8.6k
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
22
votes
1
reply
3.2k
views
Tutorial:
Introduction To R Course Materials Available
R
updated 16 months ago by
Ram
43k • written 12.1 years ago by
Sean Davis
26k
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
22
votes
2
replies
6.0k
views
Tutorial:
Use a workflow management tool to manage your computational pipelines
workflow-management
snakemake
pipeline
updated 13 months ago by
Ram
43k • written 7.5 years ago by
Eric Lim
★ 2.1k
21
votes
5
replies
6.8k
views
Tutorial:
Analysis of single-cell RNA-seq data
single-cell
RNA-Seq
updated 13 months ago by
Ram
43k • written 7.9 years ago by
Geparada
★ 1.5k
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 22 months ago by
ATpoint
82k
21
votes
26
replies
9.7k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 9 weeks ago by
Yao
▴ 30 • written 4.4 years ago by
Juke34
8.6k
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
20
votes
4
replies
14k
views
Tutorial:
How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor
affymetrix
updated 14 months ago by
Ram
43k • written 11.2 years ago by
Obi Griffith
20k
20
votes
2
replies
3.4k
views
Tutorial:
Beginner's Handbook to Next Generation Sequencing
NGS
updated 12 months ago by
Ram
43k • written 7.1 years ago by
support
▴ 650
20
votes
4
replies
8.6k
views
Tutorial:
DE analysis by edgeR
RNA-Seq
R
edgeR
updated 13 months ago by
Ram
43k • written 7.7 years ago by
zizigolu
★ 4.3k
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
20
votes
0
replies
8.8k
views
Tutorial:
Metagenomics Review Papers
metagenomics
papers
updated 14 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
20
votes
6
replies
5.7k
views
Tutorial:
Open Targets and programmatic access
open-targets
disease
API
drug
updated 14 months ago by
Ram
43k • written 7.7 years ago by
Denise CS
★ 5.2k
412 results • Page
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Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Can I perform a correlation test with 3 biological replicates per condition?
Answer: --normalizeUsing RPGC
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Comment: Sam file Header problem
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saifulislam99121
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Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
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It seems that Alexandrov's [structural variant and copy number signatures][1] estimated by the [SigProfiler software ecosystem][2] aren't c…
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Then you may want to see if a program like `lastz` ([**LINK**][1]) may be useful. [1]: https://github.com/lastz/lastz
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What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
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Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP
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bk11
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I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
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Gabriel R.
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I know about it, isn't there a simple C++ static binary?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
needle is great! but it does not handle sequences of 100k or so.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
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Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
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The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
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Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
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What do you get if you use `vg stats -a` on the GAM file?
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e.r.zakiev
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Very good question and analysis. I personally only tried SoupX so can't weigh in on the comparison. This might be not really the issue here…
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