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383 results • Page
1 of 8
Sort: Views
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Views
Votes
Replies
282
votes
39
replies
176k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 8 months ago by
Ram
41k • written 9.3 years ago by
Obi Griffith
20k
288
votes
33
replies
102k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 9 months ago by
Ram
41k • written 10.1 years ago by
Obi Griffith
20k
238
votes
176
replies
90k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 6 months ago by
Ram
41k • written 8.3 years ago by
TriS
★ 4.7k
88
votes
22
replies
83k
views
14 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 4 months ago by
sifa.khan
• 0 • written 5.4 years ago by
otwtgin2010
▴ 580
137
votes
25
replies
81k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 20 months ago by
Ram
41k • written 11.6 years ago by
Ying W
★ 4.2k
51
votes
14
replies
79k
views
10 follow
Tutorial:
Using R in Conda
R
updated 8 months ago by
Ram
41k • written 3.4 years ago by
rohitsatyam102
▴ 780
29
votes
10
replies
73k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 8 months ago by
Ram
41k • written 2.7 years ago by
Nitin Narwade
★ 1.5k
196
votes
44
replies
70k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 10 months ago by
Ram
41k • written 11.2 years ago by
Obi Griffith
20k
75
votes
13
replies
66k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r
cancer
classification
updated 13 months ago by
Ram
41k • written 10.0 years ago by
Nicholas Spies
★ 1.2k
149
votes
35
replies
61k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 9 months ago by
Ram
41k • written 11.0 years ago by
vijay
★ 1.6k
85
votes
2
replies
57k
views
6 follow
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 9 months ago by
Ram
41k • written 10.4 years ago by
Eric Normandeau
11k
146
votes
34
replies
53k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music
cancer
tcga
mutation
maf
updated 9 months ago by
Ram
41k • written 10.6 years ago by
Cyriac Kandoth
6.0k
0
votes
3
replies
50k
views
Tutorial:
Installation VMD on LINUX_64
gromacs
VMD
updated 7 months ago by
Ram
41k • written 7.5 years ago by
Hassan Rasouli
▴ 10
2
votes
1
reply
48k
views
Tutorial:
Docker denied: requested access to the resource is denied
docker
updated 16 months ago by
LauferVA
3.8k • written 16 months ago by
kodwings
▴ 20
65
votes
9
replies
48k
views
7 follow
Tutorial:
Reference Assembly - Mapping Reads To A Reference Genome
reference
samtools
mapping
bwa
updated 9 months ago by
Ram
41k • written 10.4 years ago by
Joseph Hughes
★ 3.0k
148
votes
70
replies
48k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 3 months ago by
Raheleh
▴ 260 • written 6.0 years ago by
Kevin Blighe
86k
117
votes
66
replies
44k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 8 months ago by
Ram
41k • written 5.4 years ago by
ATpoint
78k
53
votes
19
replies
43k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization
bigwig
chip-seq
rna-seq
updated 9 months ago by
Ram
41k • written 11.6 years ago by
Sukhi Singh
11k
60
votes
52
replies
42k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 8 months ago by
Ram
41k • written 7.2 years ago by
steve
★ 3.4k
95
votes
105
replies
41k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 8 months ago by
Ram
41k • written 5.2 years ago by
Kevin Blighe
86k
58
votes
25
replies
39k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 8 months ago by
Ram
41k • written 7.3 years ago by
Shicheng Guo
★ 9.3k
72
votes
3
replies
37k
views
Tutorial:
Revisiting the FastQC read duplication report
fastqc
updated 2.0 years ago by
Ram
41k • written 9.4 years ago by
Istvan Albert
99k
45
votes
2
replies
36k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
updated 9 months ago by
Ram
41k • written 11.6 years ago by
MSU course 2011
▴ 540
132
votes
123
replies
34k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 8 months ago by
1769mkc
★ 1.1k • written 5.1 years ago by
Kevin Blighe
86k
99
votes
16
replies
32k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 8 months ago by
Ram
41k • written 7.3 years ago by
Jean-Karim Heriche
26k
95
votes
25
replies
32k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
qc
trimming
fastq
updated 9 months ago by
Ram
41k • written 11.2 years ago by
Istvan Albert
99k
36
votes
14
replies
32k
views
14 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 22 days ago by
psschlogl
▴ 50 • written 3.3 years ago by
lavinia.gordon
▴ 160
90
votes
19
replies
31k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray
bioconductor
expression
classification
updated 9 months ago by
Ram
41k • written 10.1 years ago by
Obi Griffith
20k
90
votes
48
replies
31k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 26 days ago by
Ram
41k • written 10.1 years ago by
Irsan
★ 7.8k
84
votes
29
replies
30k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 4 months ago by
amziepickles
• 0 • written 7.7 years ago by
Obi Griffith
20k
142
votes
21
replies
29k
views
12 follow
Tutorial:
A few words for R beginners
Swirl
R
updated 19 months ago by
Ram
41k • written 9.0 years ago by
Parham
★ 1.6k
32
votes
12
replies
29k
views
7 follow
Tutorial:
So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control
fastqc
updated 9 months ago by
Ram
41k • written 10.1 years ago by
Istvan Albert
99k
99
votes
8
replies
28k
views
8 follow
Tutorial:
Guide to TCGA data
cancer
RNA-Seq
clinical
TCGA
updated 7 months ago by
Ram
41k • written 7.8 years ago by
Jordan Anaya
★ 1.1k
71
votes
26
replies
27k
views
15 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 9 months ago by
Ram
41k • written 9.8 years ago by
Istvan Albert
99k
73
votes
60
replies
26k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 9 months ago by
Ram
41k • written 6.2 years ago by
Kevin Blighe
86k
67
votes
6
replies
25k
views
7 follow
Tutorial:
Rna-Seq Review Papers
RNA-seq
papers
updated 9 months ago by
Ram
41k • written 11.2 years ago by
Istvan Albert
99k
104
votes
6
replies
24k
views
6 follow
Tutorial:
Creating workflows with snakemake and conda
workflow
snakemake
conda
updated 8 months ago by
Ram
41k • written 5.2 years ago by
finswimmer
16k
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 15 months ago by
Ram
41k • written 8.2 years ago by
Chirag Nepal
★ 2.4k
44
votes
6
replies
22k
views
Tutorial:
Greatly speed up conda by using mamba
software
updated 22 months ago by
cameron.cowan
▴ 40 • written 2.7 years ago by
rpolicastro
12k
51
votes
3
replies
22k
views
Tutorial:
Sam File Format - Lesser Known Tips And Tricks
sam
updated 9 months ago by
Ram
41k • written 10.9 years ago by
Ya
▴ 300
30
votes
6
replies
22k
views
Tutorial:
Transforming And Manipulating Color Space Reads
conversion
solid
updated 14 months ago by
Ram
41k • written 11.6 years ago by
Istvan Albert
99k
10
votes
5
replies
21k
views
Tutorial:
Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 8 months ago by
Ram
41k • written 5.4 years ago by
Shicheng Guo
★ 9.3k
84
votes
21
replies
20k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 8 months ago by
Ram
41k • written 3.1 years ago by
Hamid Ghaedi
3.1k
59
votes
43
replies
20k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 8 months ago by
Ram
41k • written 6.2 years ago by
Rox
★ 1.4k
34
votes
15
replies
19k
views
12 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 8 months ago by
Ram
41k • written 7.2 years ago by
martinguerrerog89
▴ 310
39
votes
6
replies
18k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 6 months ago by
Ram
41k • written 6.3 years ago by
steve
★ 3.4k
76
votes
70
replies
18k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 8 months ago by
Ram
41k • written 5.8 years ago by
Kevin Blighe
86k
42
votes
2
replies
18k
views
Tutorial:
Sequencing Technology Review Papers
sequencing
papers
updated 9 months ago by
Ram
41k • written 11.2 years ago by
Istvan Albert
99k
18
votes
40
replies
17k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 3.4 years ago by
krishdb38
• 0 • written 7.4 years ago by
Esaie
▴ 170
83
votes
34
replies
17k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 6 months ago by
adelheidkratzer
• 0 • written 5.4 years ago by
egeulgen
★ 1.3k
383 results • Page
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Recent Votes
Deeptools plotPCA on RNA-seq help
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
Answer: How should I run ssgsea analysis ?
Comment: Parsing XML file from dbGaP
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
Comment: SPAdes error: finished abnormally, OS return value: 21
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Comment: How to create a mutation frequency comparison plot?
by
rpolicastro
12k
You can make this with just ggplot. It would be two `geom_point`, a `geom_segment`, and two `geom_text` layers.
Comment: featureCounts results: low rate of 'Successfully assigned alignments'
by
GenoMax
136k
> I run a blast with the sequences and most of them belongs to globin. Globin reads shown in your FastQC report are not going to add up to…
Comment: featureCounts results: low rate of 'Successfully assigned alignments'
by
kvn95ss
▴ 20
Almost all your samples have the over represented sequence, you can blast the top 10 recurring sequences and see what it could be.
Comment: How to deeply sequence long inserts
by
GenoMax
136k
Linked read kits have not been offered by 10x genomics from last 3-4 years so that is not an option. Illumina now offers a long read tech…
Comment: Viral genes not showing up in combined mouse+virus alignment
by
GenoMax
136k
Try taking out the additional header lines from the combined GTF file. `NC_005089.1` lines should be immediately followed by `NC_001846.1` …
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
by
Nitin Narwade
★ 1.5k
Hmmmmm, okay. In this case I could think of another workaround, instead of drawing line/marks, you can add another modality to your plot, …
Comment: featureCounts results: low rate of 'Successfully assigned alignments'
by
Hamtaro
▴ 10
I added the fastQC. What do you think of the possible cause I have proposed?
Comment: Problem in installing 'magick' R package
by
Jean-Karim Heriche
26k
This isn't a bioinformatics question. What do you mean by "install all the dependencies"? Did you read the error message? It's telling you …
Comment: Problem in installing 'magick' R package
by
DBScan
▴ 200
Have you read the error message? it tells you to try installing the Magick++ library: ``` Try installing: deb: libmagick++-dev (Debian, …
Answer: FVA on Sybil
by
Thomas
• 0
The first half of this vector should be your minimal fluxes per reaction and the second half your maximal fluxes per reaction. Thus this ve…
Comment: AttributeError: module 'collections' has no attribute 'Hashable'
by
jiyoung
▴ 20
Currently I am experiencing the same problem. Have you solved this?
Comment: Help doing differential expression analysis -experimental design and gProfiler T
by
rajabolacuan
• 0
Good Information Sir
Comment: Viral genes not showing up in combined mouse+virus alignment
by
cook.675
▴ 200
Hello I was curious to follow up and wonder if anyone knew why the viral genes are not showing up in the count matrix? I can't seem to solv…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
CTLong
▴ 10
That makes sense. Thanks for the reminder.
Comment: bwa mem hangs after a few thousand reads
by
GenoMax
136k
Then you probably are best served by talking with your local sys admins to see where the issue may be.
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