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117,134 results • Page 3 of 2343
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19
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43
replies
5.7k
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Annotation of huge number of CNV files
CNV annotation TCGA
5.8 years ago by nazaninhoseinkhan ▴ 520
57
votes
43
replies
16k
views
8 follow
Forum: Best RNA-Seq aligner: A comparison of mapping tools
NGS alignment genome RNA-Seq sequence
updated 14 months ago by 44k • written 5.3 years ago by 11k
103
votes
42
replies
31k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 6 weeks ago by 22k • written 10.5 years ago by ★ 3.6k
11
votes
42
replies
4.2k
views
over presented kmer in fastq
fastqc RNA-Seq
6.6 years ago by Sam ▴ 150
57
votes
42
replies
6.7k
views
12 follow
Forum: Why is academic software hard to install?
software-installation
updated 2.3 years ago by 44k • written 9.6 years ago by 33k
138
votes
42
replies
22k
views
22 follow
Forum: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 14 months ago by 4.2k • written 11.0 years ago by ★ 1.6k
152
votes
42
replies
181k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 2.0 years ago by 44k • written 12.2 years ago by 20k
28
votes
42
replies
7.2k
views
7 follow
How to add tophat and bowtie to the path?
export PATH bowtie2.2.9 tophat2
7.5 years ago by mirza ▴ 180
8
votes
42
replies
4.8k
views
NaS (Nanopore Synthetic-long) help
Assembly preprocessing
updated 16 months ago by 44k • written 9.0 years ago by ▴ 290
23
votes
41
replies
4.5k
views
6 follow
I want to correct the erroneous barcode file, and the Python code that I've written, using Biopython, is very slow. How can I make this process fast…
NGS biopython illumina WGS
updated 12 months ago by 44k • written 13 months ago by ▴ 30
31
votes
41
replies
2.8k
views
12 follow
Forum: Question regarding journal publications
publications journals
updated 11 months ago by 44k • written 4.2 years ago by ▴ 40
98
votes
41
replies
6.3k
views
17 follow
Forum: I am really pissed off by the bioinformatics software world. Do/can we have a better solution?
software-error next-gen-sequencing
updated 13 months ago by 44k • written 7.7 years ago by ▴ 510
38
votes
41
replies
60k
views
9 follow
Volcano Plot from DEseq2
R
written 6.5 years ago by ★ 1.2k
171
votes
41
replies
99k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 8 months ago by 44k • written 13.0 years ago by ▴ 250
16
votes
41
replies
9.7k
views
How to extract information from headers of fasta file
sequence
updated 23 months ago by 44k • written 9.2 years ago by ▴ 70
18
votes
41
replies
3.7k
views
6 follow
Convert amino acid sequences into nucleotide sequences
nucleotide protein
updated 5 months ago by 21k • written 7 months ago by ▴ 40
18
votes
41
replies
14k
views
6 follow
paired end illumina reads
Assembly paired end
updated 22 months ago by 44k • written 8.6 years ago by ▴ 290
5
votes
41
replies
3.0k
views
Insert sequence in nt database
nt
4.0 years ago by anasofiamoreira94 ▴ 80
13
votes
41
replies
2.5k
views
Is my file created completely
sam BWA-MEM BWA
updated 14 months ago by 44k • written 7.0 years ago by ▴ 10
203
votes
41
replies
25k
views
20 follow
Forum: Genomics is not Special. Computational Biologists are reinventing the wheel for big data biology analysis
genomics cram gatk galaxy
updated 15 months ago by 44k • written 9.5 years ago by ★ 5.3k
26
votes
41
replies
17k
views
10 follow
WGCNA modules and categorical traits relationship
WGCNA
updated 18 months ago by • 0 • written 6.4 years ago by ▴ 120
19
votes
41
replies
9.3k
views
7 follow
n.sv number for batch effects in RNA-seq
RNA-Seq
updated 6.8 years ago by ★ 5.2k • written 6.8 years ago by ▴ 80
18
votes
40
replies
19k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 3.9 years ago by • 0 • written 7.9 years ago by ▴ 170
68
votes
40
replies
6.5k
views
11 follow
Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
next-gen sequencing sequencing
updated 12.6 years ago by ▴ 310 • written 12.6 years ago by ★ 1.3k
40
votes
40
replies
11k
views
9 follow
What is the reason for trimming reads to 30 bp for ATAC-seq aligning?
ATAC-seq alignment
updated 6.3 years ago by 88k • written 7.6 years ago by ▴ 560
16
votes
40
replies
6.4k
views
About TCGA CNV data preprocessing
SNP CNV
updated 5.6 years ago by 88k • written 5.6 years ago by ▴ 50
6
votes
40
replies
11k
views
Fastx_Collapser Has No Fastq Output
fastx RNA-seq
updated 15 months ago by 44k • written 10.7 years ago by ▴ 240
67
votes
40
replies
9.8k
views
12 follow
Forum: I want to re-open the old debate: python or perl ?
perl python
updated 2.3 years ago by 44k • written 9.5 years ago by ★ 2.9k
10
votes
40
replies
6.6k
views
weird insert size post trimming
RNA-Seq
updated 6.8 years ago by ★ 2.9k • written 6.8 years ago by ▴ 290
151
votes
39
replies
25k
views
20 follow
Forum: A Farewell To Bioinformatics
bioinformatics
updated 15 months ago by 44k • written 11.3 years ago by 3.0k
20
votes
39
replies
10.0k
views
7 follow
Is Blast+ Running As Fast As It Could ?
blast blast memory
updated 8.7 years ago by ▴ 170 • written 12.4 years ago by ▴ 160
288
votes
39
replies
184k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 14 months ago by 44k • written 9.7 years ago by 20k
11
votes
39
replies
4.2k
views
Any advice for a de novo genome assembly
k-mer de novo genome assembly
updated 7.5 years ago by ▴ 60 • written 7.5 years ago by ▴ 640
25
votes
39
replies
5.9k
views
8 follow
Forum: Bioinformatics Study Group
study-group
updated 15 months ago by 44k • written 10.9 years ago by ▴ 440
66
votes
39
replies
7.6k
views
13 follow
What Do You Consider The Most Trivial And The Most Challenging Tasks In Your Particular Field Of Work?
career subjective
updated 3.2 years ago by 44k • written 14.2 years ago by ▴ 310
69
votes
39
replies
4.8k
views
14 follow
Forum: Preparation for Bioinformatics.SE closing
meta biostars
updated 12 months ago by 44k • written 7.0 years ago by 13k
18
votes
39
replies
4.4k
views
Tool: CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 12 months ago by 44k • written 5.1 years ago by ▴ 50
98
votes
39
replies
159k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 13 months ago by ▴ 180 • written 11.9 years ago by ▴ 390
55
votes
39
replies
5.9k
views
8 follow
Programming Challenge - Synthetic Whole Genome Vcf
vcf python perl awk
updated 11.7 years ago by 8.3k • written 11.7 years ago by ▴ 310
226
votes
39
replies
289k
views
33 follow
Gene Id Conversion Tool
david
updated 7 months ago by 44k • written 14.6 years ago by ▴ 620
36
votes
39
replies
4.2k
views
11 follow
Forum: Survey/Vote: If you could double the speed of any three commandline tools, which three would they be?
blast RNA-Seq alignment next-gen-sequencing
updated 12 months ago by 44k • written 6.5 years ago by ▴ 130
81
votes
39
replies
7.7k
views
11 follow
News: State Of Biostar - Future Directions (January 2013)
biostars
updated 15 months ago by 44k • written 11.4 years ago by 100k
78
votes
38
replies
33k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 12 weeks ago by ▴ 60 • written 7.9 years ago by 6.6k
27
votes
38
replies
20k
views
Heatmap based with FPKM values
RNA-Seq next-gen R
updated 5.0 years ago by 20 • written 6.5 years ago by ▴ 820
53
votes
38
replies
4.6k
views
10 follow
Multiple alignment software
alignment clustal omega tcoffee
updated 4.7 years ago by 100k • written 4.7 years ago by ▴ 130
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 2.1 years ago by 44k • written 9.3 years ago by ▴ 920
48
votes
38
replies
17k
views
8 follow
Forum: Eukaryotic Genome Annotation in 2016
software genome annotation
updated 13 months ago by 44k • written 8.2 years ago by 11k
231
votes
38
replies
147k
views
29 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl genome-coordinates liftover
updated 11 months ago by 44k • written 11.2 years ago by 20k
39
votes
38
replies
9.1k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 21 months ago by 44k • written 8.5 years ago by 13k
129
votes
38
replies
8.4k
views
21 follow
Forum: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 12 months ago by 44k • written 5.1 years ago by 100k
117,134 results • Page 3 of 2343
Recent Votes
Low DESeq2 Sensivity on scRNA Pseudobulk Samples
DESEQ2: How can I convert ensembl gene id's to HGNC gene names.
Problem with Ensembl version identifiers after running DESeq2
Issues with adding gene name and entrez ID to DESeq2 result having Ensembl ID.
A: Looking for differential gene expression between treatment, within a specific cl
How to compare cell-type ratios in sc-RNA seq data?
How to calculate cell type frequency between two groups in single cell data
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Recent Replies
Comment: Merging multiple samples in Seurat by Picasa ▴ 640
did you split by sample or donor ?
Comment: Harmony integration group.by.var parameter by Picasa ▴ 640
For downstream analysis, after integration, my plan is to annotate each cluster/cell type and then perform a DGE analysis of KO versus WT f…
Comment: How to calculate cell type frequency between two groups in single cell data by Bastien Hervé 5.3k
That is correct
Answer: Setting a threshold on gene expression for subsetting (scRNA-seq) by ATpoint 82k
That depends on the data and the marker. Generally I would plot violins per cluster for the marker(s) and see whether one robustly overexpr…
Comment: Error when i use EVidenceModeler to do the genome annotation by peanut • 0
thank you so much ,i get it
Comment: Number of non-ATCG nucleotides replaced by Salmon by Tonya S. ▴ 10
Oops, yes, that must be where they are coming from. For some reason, I was thinking the genome was just soft-masked. How embarrassing! Than…
Answer: Number of non-ATCG nucleotides replaced by Salmon by Rob 6.6k
If there are no other signs that anything is awry, I probably wouldn't worry about this. Is it possible that these non-canonical nucleotid…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage by Brian Bushnell 20k
I examined nine 10B runs and five 25B runs (we just started getting 25B flowcells a few months ago). I did not pay close attention but it …
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage by GenoMax 142k
> I don't know how widespread these issues are outside of JGI. Very few small/medium sequencing centers likely have NovaSeq X. This is the…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage by Brian Bushnell 20k
Supporting figures, taken from some slides I prepared for internal use. HDist 0, 1, and 2 correspond to 0, 1, and 2 mismatches allowed in …
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
This works. Thank you so so much!
Comment: Harmony integration group.by.var parameter by jared.andrews07 ★ 17k
>I am not sure, but using "Sample_ID" might remove the differences between the conditions right ? More than likely, it'd at least impact t…
Comment: Harmony integration group.by.var parameter by Picasa ▴ 640
Thanks jared.andrews07 for your answer. So, you are suggesting to use only "Donor" in the integration? ```r RunHarmony(seu_obj, group.by.…
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea by sc_analysis • 0
I am not sure what should be the cut off. Looking at the vlnplot before subsetting i thought most of the cells are falling under 7500 nfeat…
Comment: How to calculate cell type frequency between two groups in single cell data by Sara ▴ 30
Thank you for your comment and sorry if this question might be so basic. How can I normalize the number of cells? If I am not wrong the i…
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