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408 results • Page
1 of 9
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Votes
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239
votes
176
replies
94k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 10 months ago by
Ram
43k • written 8.7 years ago by
TriS
★ 4.7k
133
votes
123
replies
37k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 12 months ago by
1769mkc
★ 1.2k • written 5.4 years ago by
Kevin Blighe
87k
97
votes
105
replies
45k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 12 months ago by
Ram
43k • written 5.6 years ago by
Kevin Blighe
87k
76
votes
70
replies
19k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 12 months ago by
Ram
43k • written 6.1 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 6.3 years ago by
Kevin Blighe
87k
117
votes
66
replies
46k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 12 months ago by
Ram
43k • written 5.7 years ago by
ATpoint
81k
73
votes
60
replies
27k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 13 months ago by
Ram
43k • written 6.6 years ago by
Kevin Blighe
87k
60
votes
52
replies
43k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 12 months ago by
Ram
43k • written 7.5 years ago by
steve
★ 3.5k
90
votes
48
replies
33k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 4 months ago by
Ram
43k • written 10.4 years ago by
Irsan
★ 7.8k
72
votes
48
replies
17k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 13 months ago by
Ram
43k • written 11.1 years ago by
lh3
33k
196
votes
44
replies
71k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 14 months ago by
Ram
43k • written 11.5 years ago by
Obi Griffith
20k
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 12 months ago by
Ram
43k • written 6.5 years ago by
Rox
★ 1.4k
18
votes
40
replies
18k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 3.7 years ago by
krishdb38
• 0 • written 7.8 years ago by
Esaie
▴ 170
287
votes
39
replies
182k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 12 months ago by
Ram
43k • written 9.6 years ago by
Obi Griffith
20k
149
votes
35
replies
62k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 13 months ago by
Ram
43k • written 11.3 years ago by
vijay
★ 1.6k
83
votes
34
replies
18k
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
147
votes
34
replies
54k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music
cancer
tcga
mutation
maf
updated 13 months ago by
Ram
43k • written 11.0 years ago by
Cyriac Kandoth
6.0k
296
votes
33
replies
107k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 13 months ago by
Ram
43k • written 10.4 years ago by
Obi Griffith
20k
14
votes
31
replies
6.6k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
geneset
genome
gene
abinitio
updated 12 months ago by
Ram
43k • written 4.6 years ago by
Juke34
8.5k
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 6.2 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 42 minutes 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 14 days ago by
jkbonfield
★ 1.2k • written 5.1 years ago by
finswimmer
16k
84
votes
29
replies
31k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 8 months ago by
amziepickles
• 0 • written 8.1 years ago by
Obi Griffith
20k
73
votes
27
replies
27k
views
16 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 3 months ago by
snardeli
• 0 • written 10.1 years ago by
Istvan Albert
100k
21
votes
26
replies
9.4k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 13 days ago by
Yao
▴ 30 • written 4.3 years ago by
Juke34
8.5k
64
votes
26
replies
14k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 12 months ago by
Ram
43k • written 6.5 years ago by
Kevin Blighe
87k
58
votes
25
replies
40k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 12 months ago by
Ram
43k • written 7.7 years ago by
Shicheng Guo
★ 9.4k
139
votes
25
replies
83k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 24 months ago by
Ram
43k • written 11.9 years ago by
Ying W
★ 4.2k
95
votes
25
replies
33k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
qc
trimming
fastq
updated 13 months ago by
Ram
43k • written 11.5 years ago by
Istvan Albert
100k
93
votes
23
replies
90k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 9 weeks ago by
clara.apicella
• 0 • written 5.7 years ago by
otwtgin2010
▴ 610
85
votes
21
replies
22k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 12 months ago by
Ram
43k • written 3.5 years ago by
Hamid Ghaedi
3.2k
142
votes
21
replies
30k
views
12 follow
Tutorial:
A few words for R beginners
Swirl
R
updated 23 months ago by
Ram
43k • written 9.3 years ago by
Parham
★ 1.6k
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 12 months ago by
Ram
43k • written 4.8 years ago by
jared.andrews07
★ 16k
8
votes
19
replies
13k
views
9 follow
Tutorial:
A:orthomcl with local mysql server on linux server, complete install
mysql
orthomcl
updated 12 months ago by
Ram
43k • written 9.4 years ago by
Lesley Sitter
▴ 600
23
votes
19
replies
6.8k
views
10 follow
Tutorial:
MutScan: Detect important mutations by scanning FastQ files directly
fastq
mutation
cancer
target
updated 11 months ago by
Ram
43k • written 7.5 years ago by
chen
★ 2.5k
90
votes
19
replies
32k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray
bioconductor
expression
classification
updated 13 months ago by
Ram
43k • written 10.4 years ago by
Obi Griffith
20k
42
votes
19
replies
7.8k
views
8 follow
Tutorial:
Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 13 months ago by
Ram
43k • written 11.1 years ago by
Daniel Standage
4.1k
53
votes
19
replies
43k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization
bigwig
chip-seq
rna-seq
updated 13 months ago by
Ram
43k • written 12.0 years ago by
Sukhi Singh
11k
47
votes
19
replies
13k
views
8 follow
Tutorial:
Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control
fastqc
updated 14 months ago by
Ram
43k • written 11.1 years ago by
Istvan Albert
100k
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 10 months ago by
GenoMax
140k • written 10.4 years ago by
Obi Griffith
20k
26
votes
17
replies
7.7k
views
8 follow
Tutorial:
virtualenv - running Python based software in isolation
python
virtualenv
updated 18 months ago by
Ram
43k • written 9.6 years ago by
Ian
6.0k
12
votes
17
replies
2.9k
views
Tutorial:
How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola
bwa
updated 15 months ago by
Ram
43k • written 8.8 years ago by
Istvan Albert
100k
8
votes
17
replies
3.1k
views
Tutorial:
Simple approach to RNA-seq (T-Bioinfo platform)
alignment
next-gen-sequencing
RNA-seq
updated 19 months ago by
Ram
43k • written 8.5 years ago by
elia.brodsky
▴ 340
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 9 days ago by
aUser
▴ 30 • written 7.5 years ago by
martinguerrerog89
▴ 310
42
votes
16
replies
23k
views
15 follow
Tutorial:
Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC
varscan2
CNV
copy-number
updated 19 months ago by
Ram
43k • written 8.5 years ago by
Chirag Nepal
★ 2.4k
99
votes
16
replies
33k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 12 months ago by
Ram
43k • written 7.6 years ago by
Jean-Karim Heriche
27k
39
votes
16
replies
35k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 3 months ago by
GenoMax
140k • written 3.6 years ago by
lavinia.gordon
▴ 160
25
votes
15
replies
8.8k
views
8 follow
Tutorial:
Syllabus To Learn Bioinformatics From Online Video Resources
course
training
mooc
updated 13 months ago by
Ram
43k • written 11.2 years ago by
Medhat
9.7k
63
votes
15
replies
14k
views
Tutorial:
Which human reference genome should I use?
assembly
genome
alignment
updated 10 months ago by
Ram
43k • written 5.5 years ago by
finswimmer
16k
34
votes
15
replies
6.4k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 12 months ago by
Ram
43k • written 4.8 years ago by
Shicheng Guo
★ 9.4k
408 results • Page
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Recent Votes
A: Crispr-cas9 screen analysis mageck
A: Crispr-cas9 screen analysis mageck
Crispr-cas9 screen analysis mageck
Comment: Issue with making local BLAST database
Comment: struggle to get fasta files from ucsc goldenPath
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
Quantile normalizing prior to or after TPM scaling?
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Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Of course ... But as 'expected' the range `range=chr8:127794533-128101253` in the output sequence file belongs to: LF385466, LF385467, MA62…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Can you select the output format as sequence instead of BED?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Could you please elaborate how to retrieve the sequences directly from the table browser? Thanks!
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If coordinates in your BED file refer to chromosomal locations then you need to use the whole genome file and get those sections by the met…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
Istvan Albert
100k
maybe it would work better to ask the OP to post their question as a new one and delete this answer after, if you delete the post they ca…
Comment: Issue with making local BLAST database
by
GenoMax
140k
By default only 20 entries are returned if you don't set the `retmax` parameter. You will not want to do this via R since you will be limit…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
So this is my approach: I want to interrogate gene PVT1, I know the coordinates for it is chr8:127794532-128101252 In UCSC table I selected…
Comment: Flow Cytometry Data Analysis by Seurat
by
ATpoint
81k
> I think Seurat is suitable for our purpose (e.g. conducting dimensional reduction of the data such as tSNE), but does it make sense? No…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
mRNA file is not going to have the same co-ordinates as the main chromosomes. Can you clarify what coordinates are in your BED file?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
It is because I want to pull the mRNA fasta files and not DNA (which I guess is the case if I pull it from the entire genome)
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If your intervals are for main chromosomes why are you using the mRNA file instead of the entire genome? If you have the gene ID's you coul…
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
by
Pierre Lindenbaum
160k
I downsampled the bams and it works now...
Answer: ONT direct RNA sequencing
by
dthorbur
★ 1.7k
You can check the validity of gzipped files using `gzip -v -t file.gz`. Should look something like this: ``` $ gzip -v -t test_file.…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
I tested seqtk sample but I generate a wird result. Can I share my code and results with you please ?
Comment: Nextflow ERROR : Timeout waiting for connection from pool
by
GenoMax
140k
As best as I can tell it is a combination of things. Did you try setting `export NXF_ENABLE_VIRTUAL_THREADS="true"` in your shell? You also…
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