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75
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13
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67k
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10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 17 months ago by 43k • written 10.4 years ago by ★ 1.2k
138
votes
33
replies
66k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 18 months ago by 43k • written 10.0 years ago by ▴ 490
138
votes
22
replies
65k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene LIMMA edgeR
updated 10 months ago by 87k • written 6.4 years ago by ★ 1.9k
63
votes
22
replies
64k
views
16 follow
How To Convert Gencode Gtf Into Bed Format ?
gtf bed
updated 16 months ago by • 0 • written 11.5 years ago by ★ 1.5k
13
votes
13
replies
64k
views
pheatmap: Error in hclust(d, method = method) : NA/NaN/Inf in foreign function call (arg 10)
R RNA-Seq pheatmap arg10
updated 3.3 years ago by ▴ 40 • written 3.8 years ago by ▴ 160
328
votes
54
replies
64k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 5 months ago by 43k • written 14.1 years ago by 24k
40
votes
7
replies
63k
views
Clustering Data (Rna-Seq) Using R To Produce A Heatmap
r rna heatmap clustering gene
updated 22 months ago by 43k • written 12.4 years ago by ▴ 450
31
votes
11
replies
63k
views
samtools sort bam file
ChIP-Seq
updated 5.9 years ago by 47k • written 5.9 years ago by ▴ 120
36
votes
14
replies
63k
views
9 follow
What Is The Difference Between Hg18 And Hg19?
genome hg hg
updated 12.2 years ago by 14k • written 12.2 years ago by ▴ 170
1
vote
6
replies
63k
views
Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed
R
updated 13 months ago by 43k • written 7.3 years ago by • 0
100
votes
6
replies
63k
views
6 follow
Insert Size And Fragment Size ?
2.5 years ago by Nicolas Rosewick 10k
159
votes
24
replies
62k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
alternative-splicing splicing rna-seq
updated 10 months ago by 43k • written 11.1 years ago by 10k
39
votes
20
replies
62k
views
8 follow
How to convert to .SRA files to .FQ (FASTQ)
fastq FASTQ sra RNA-Seq SRAA
updated 2.2 years ago by ▴ 20 • written 9.7 years ago by ▴ 50
16
votes
14
replies
62k
views
7 follow
Convert SAM to BAM
sam RNA-Seq bam
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 90
91
votes
25
replies
62k
views
18 follow
Best Practices/Softwares To Calculate Ka/Ks Ratio
kaks selection software
updated 19 months ago by 54k • written 13.2 years ago by 3.4k
149
votes
35
replies
62k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 14 months ago by 43k • written 11.4 years ago by ★ 1.6k
25
votes
5
replies
62k
views
7 follow
Rpkm Calculation For Genes
rpkm rna-seq
updated 11.5 years ago by 13k • written 11.5 years ago by ▴ 270
53
votes
20
replies
62k
views
14 follow
Bam Header Edit
bam
updated 20 months ago by 43k • written 11.9 years ago by 12k
53
votes
8
replies
62k
views
8 follow
What Is A Good Threshold For Log2 Fold Change?
microarray gene
updated 9.1 years ago by 20 • written 13.1 years ago by ▴ 90
102
votes
30
replies
62k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment
updated 5 months ago by 43k • written 14.1 years ago by ★ 1.0k
39
votes
5
replies
61k
views
Idenity, e value or bitscore ?
blast annotation
updated 4.9 years ago by ▴ 310 • written 8.0 years ago by ▴ 70
19
votes
2
replies
61k
views
Keeping pheatmap colour range the same for different data sets
R RNA-Seq pheatmap
updated 7.9 years ago by ▴ 620 • written 7.9 years ago by ▴ 60
27
votes
21
replies
61k
views
21 follow
Public Electronic Health Records Database
database
updated 2.6 years ago by 43k • written 11.0 years ago by ★ 1.6k
77
votes
24
replies
61k
views
16 follow
How To Sort Bed Format File
bed
updated 18 months ago by 161k • written 11.2 years ago by ▴ 450
164
votes
70
replies
60k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq next-gen-sequencing
updated 22 days ago by 43k • written 12.8 years ago by ★ 1.8k
90
votes
44
replies
60k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 24 months ago by 43k • written 13.0 years ago by ★ 3.4k
48
votes
10
replies
60k
views
7 follow
RNA-seq: Explain STAR quantMode geneCounts values
RNA-Seq STAR Differential expression
updated 6.0 years ago by ▴ 530 • written 7.5 years ago by ▴ 370
2
votes
1
reply
60k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 21 months ago by 4.2k • written 21 months ago by ▴ 20
93
votes
19
replies
59k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 10 months ago by 43k • written 13.6 years ago by ★ 2.6k
2
votes
10
replies
59k
views
R: remove rows by a list of rownames
R
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 50
38
votes
41
replies
59k
views
9 follow
Volcano Plot from DEseq2
R
written 6.4 years ago by ★ 1.2k
17
votes
6
replies
59k
views
Turn Off Blast Search On Reverse Complement Strand In Blastn
blast sequence
updated 6 months ago by 43k • written 14.2 years ago by ★ 1.4k
52
votes
8
replies
59k
views
7 follow
Subsampling Bam File With Samtools
bam samtools
updated 3 months ago by ▴ 10 • written 10.8 years ago by ▴ 250
0
votes
6
replies
59k
views
Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
R heatmap error
updated 2.9 years ago by • 0 • written 5.1 years ago by ▴ 50
1.2k
votes
206
replies
59k
views
108 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 10 months ago by ★ 1.4k • written 13.1 years ago by 22k
87
votes
2
replies
59k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 13 months ago by 43k • written 10.8 years ago by 11k
65
votes
12
replies
58k
views
7 follow
Recommended cutoff for FDR - 0.05 or 0.1
RNA-Seq R
updated 3.1 years ago by • 0 • written 7.6 years ago by ▴ 180
45
votes
9
replies
58k
views
FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
next-gen RNA-Seq single-cell R
updated 8 months ago by ▴ 160 • written 4.4 years ago by ▴ 160
8
votes
3
replies
58k
views
what is the difference between single end and paired end in sequencing
RNA-Seq
updated 2.5 years ago by 43k • written 9.8 years ago by ▴ 660
28
votes
22
replies
57k
views
11 follow
How To Convert List Of Entrez Ids Into Gene Name
r genomics entrez
updated 9 months ago by • 0 • written 11.0 years ago by ▴ 90
64
votes
24
replies
57k
views
20 follow
Download All The Bacterial Genomes From Ncbi
ncbi
updated 2.2 years ago by 43k • written 11.3 years ago by ▴ 290
50
votes
13
replies
56k
views
13 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 6 months ago by ▴ 160 • written 8.3 years ago by ▴ 490
61
votes
23
replies
56k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam mapping
updated 5 months ago by ★ 1.2k • written 11.1 years ago by ★ 1.3k
87
votes
12
replies
56k
views
9 follow
What are chimeric reads?
sequence
updated 2.2 years ago by 43k • written 9.5 years ago by ▴ 300
30
votes
8
replies
56k
views
7 follow
R: How to convert log2FC (Fold Change) obtained by limma's topTable() function to FC
limma microarray topTable R
updated 21 months ago by 43k • written 9.9 years ago by ★ 4.1k
15
votes
5
replies
56k
views
R Help: For Loop Over Range Of Number And Calculate Average Using An If Statement
r
updated 8.3 years ago by 20 • written 10.2 years ago by ▴ 110
80
votes
27
replies
56k
views
20 follow
How To Write Data In A Granges Object To A Bed File.
bed
updated 19 months ago by ▴ 70 • written 10.3 years ago by ▴ 190
72
votes
18
replies
55k
views
13 follow
Extracting Multiple Fasta Sequences At A Time From A File Containing Many Sequences
fasta sequence parsing perl
updated 13.5 years ago by 6.0k • written 13.5 years ago by ▴ 110
95
votes
5
replies
55k
views
Difference between Hard Clip and Soft Clip in Samtools CIGAR string
samtools clipped-reads soft-clip bam hard-clip
updated 2.3 years ago by 43k • written 9.7 years ago by ★ 2.5k
12
votes
7
replies
55k
views
Use Python To List Filename With Specific Extensions.
python
updated 12.8 years ago by 28k • written 12.8 years ago by ★ 1.7k
116,495 results • Page 3 of 2330
Recent Votes
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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