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222
votes
38
replies
266k
views
31 follow
Gene Id Conversion Tool
mapping conversion
updated 17 months ago by ▴ 90 • written 11.8 years ago by ▴ 620
54
votes
3
replies
212k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
RNA-Seq expression gene protein Tutorial
updated 4.1 years ago by ▴ 230 • written 7.2 years ago by ▴ 880
231
votes
29
replies
196k
views
23 follow
How To Filter Mapped Reads With Samtools
samtools
updated 3 months ago by • 0 • written 8.7 years ago by ▴ 530
298
votes
77
replies
177k
views
49 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 3.0 years ago by 45k • written 10.5 years ago by 4.8k
43
votes
23
replies
163k
views
23 follow
How To Update R In Ubuntu ?
r ubuntu
updated 14 months ago by ▴ 50 • written 7.6 years ago by ▴ 210
149
votes
42
replies
162k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 2.1 years ago by • 0 • written 9.4 years ago by 19k
117
votes
19
replies
154k
views
13 follow
What'S The Difference Between Cds And Orf?
cds orf
updated 12 weeks ago by • 0 • written 9.1 years ago by ▴ 330
135
votes
14
replies
149k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen sequencing
updated 20 months ago by ★ 2.0k • written 11.3 years ago by 137k
51
votes
11
replies
146k
views
6 follow
How To Deal With Duplicate Row Names Error In R
r
updated 8.5 years ago by 49k • written 8.5 years ago by ▴ 860
151
votes
19
replies
141k
views
9 follow
Forward And Reverse Strand Conventions
sequence strand
updated 10.5 years ago by 49k • written 10.7 years ago by ★ 2.7k
117
votes
9
replies
133k
views
8 follow
How Can I Convert Bam To Sam?
next-gen sequencing bam sam conversion
updated 7.7 years ago by 21k • written 11.0 years ago by 4.8k
257
votes
40
replies
131k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
GEO SRA fastq bam download Tutorial
updated 5 weeks ago by 34k • written 6.9 years ago by 19k
117
votes
19
replies
126k
views
14 follow
Blast - Formatting Output
blast format output
updated 10 months ago by • 0 • written 7.6 years ago by ▴ 250
344
votes
80
replies
125k
views
32 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
tools parallel next-gen ngs Tool
7 months ago by ole.tange ★ 4.0k
109
votes
28
replies
123k
views
15 follow
Correct Way To Parse A Fasta File In Python
fasta parsing python
updated 2.9 years ago by 34k • written 11.3 years ago by 11k
10
votes
4
replies
120k
views
How To Count The Number Of Elements In A Column Other Than 'X' In R
r programming
updated 10.0 years ago by 4.2k • written 10.0 years ago by ▴ 20
205
votes
31
replies
115k
views
24 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome coordinates conversion liftover ensembl Tool
updated 3 months ago by ▴ 200 • written 8.4 years ago by 19k
26
votes
10
replies
112k
views
Calculating P-Values From Z-Scores
statistics r
updated 2.8 years ago by 75k • written 9.5 years ago by ▴ 860
22
votes
9
replies
111k
views
8 follow
How to calculate "fold changes" in gene expression?
R gene
updated 4.9 years ago by ▴ 30 • written 6.2 years ago by ▴ 70
127
votes
32
replies
110k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 2.3 years ago by • 0 • written 10.4 years ago by ▴ 520
111
votes
25
replies
109k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human fasta sequence bwa
updated 4.5 years ago by ▴ 160 • written 11.0 years ago by 4.8k
115
votes
21
replies
107k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python perl comparison
updated 9.4 years ago by ▴ 30 • written 9.7 years ago by ★ 2.5k
125
votes
8
replies
104k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf tabix
updated 2.9 years ago by 10k • written 8.6 years ago by ▴ 370
130
votes
30
replies
103k
views
25 follow
Useful Bash Commands To Handle Fasta Files
command-line command-line fasta list bash
updated 9 weeks ago by ▴ 70 • written 9.4 years ago by ★ 2.8k
28
votes
8
replies
103k
views
7 follow
How To Calculate Fpkm (Fragments Per Kilobase Of Exon Per Million Fragments Mapped)
rna fpkm rpkm
written 10.4 years ago by ▴ 210
88
votes
10
replies
102k
views
11 follow
Best Way To Do Pathway Analysis Of A Set Of Genes?
protein genes pathway analysis function
updated 9.3 years ago by ★ 2.5k • written 9.3 years ago by ★ 1.0k
3
votes
3
replies
101k
views
Find mismatch in two columns in a data frame in R
R
updated 5.4 years ago by ▴ 10 • written 5.4 years ago by ▴ 20
46
votes
10
replies
101k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm rpkm rna-seq
updated 20 months ago by ★ 2.0k • written 8.3 years ago by ★ 1.5k
10
votes
6
replies
100k
views
How can I uninstall my packages in Rstudio
R Bioconductor
updated 10 months ago by 10k • written 3.5 years ago by ▴ 30
145
votes
52
replies
98k
views
28 follow
Fastq Convert To Fasta
perl
updated 20 months ago by ▴ 50 • written 7.7 years ago by ★ 1.3k
12
votes
8
replies
96k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 5.4 years ago by ▴ 780 • written 9.7 years ago by ▴ 490
115
votes
15
replies
95k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 10.5 years ago by • 0 • written 10.7 years ago by ▴ 190
31
votes
8
replies
95k
views
8 follow
How Do You Start Writing An Algorithm? Help Needed!
java structure algorithm
updated 10.5 years ago by • 0 • written 11.2 years ago by ▴ 70
84
votes
9
replies
90k
views
9 follow
How To Merge Two Fastq.Gz Files?
merge fastq
updated 7.8 years ago by 137k • written 7.8 years ago by ▴ 730
74
votes
37
replies
89k
views
17 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 5 days ago by • 0 • written 9.1 years ago by ▴ 330
106
votes
7
replies
87k
views
Bam And Indexed Bam Files
bam index
9.6 years ago by Sahel ▴ 220
166
votes
30
replies
81k
views
17 follow
What Is The Best Method To Find Orthologous Genes Of A Species?
orthologues
updated 6.8 years ago by ★ 2.5k • written 10.3 years ago by ▴ 560
93
votes
19
replies
77k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence ucsc fasta
updated 5.2 years ago by ▴ 10 • written 11.4 years ago by 27k
57
votes
11
replies
74k
views
8 follow
Blog: Gene expression units explained: RPM, RPKM, FPKM and TPM
RNA-Seq gene expression Blog
3.0 years ago by Renesh ★ 2.0k
43
votes
15
replies
74k
views
9 follow
How Do I Count The Number Values Less Than X In A Column Using R ?
rna edger r counts
updated 6.7 years ago by 8.2k • written 10.3 years ago by ▴ 900
87
votes
13
replies
74k
views
13 follow
Convertion Of Gff3 To Gtf
gff gtf
updated 11 weeks ago by ▴ 790 • written 9.2 years ago by 11k
56
votes
14
replies
73k
views
10 follow
What Does Samtools Flagstat Results Mean?
rna samtools mouse
updated 5.0 years ago by ▴ 120 • written 9.8 years ago by ▴ 440
112
votes
8
replies
72k
views
GRCh37/38(NCBI) vs hg19/hg38(UCSC)
ncbi ucsc grch38 hg38
updated 6.8 years ago by ★ 5.1k • written 6.9 years ago by ▴ 470
98
votes
16
replies
72k
views
15 follow
How Much Coverage Do We Need For An Rna-Seq Experiment?
rna-seq coverage
6.7 years ago by Obi Griffith 19k
183
votes
43
replies
72k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome visualization ideogram
updated 3.7 years ago by ★ 3.1k • written 11.4 years ago by ★ 1.6k
78
votes
29
replies
71k
views
20 follow
How To Split A Bam File By Chromosome
bam split chromosome
updated 2 days ago by • 0 • written 9.1 years ago by ▴ 350
232
votes
32
replies
70k
views
22 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates tutorial Tutorial
updated 5 months ago by ▴ 10 • written 7.8 years ago by 19k
229
votes
175
replies
70k
views
72 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq TCGA Survival Tutorial
updated 4 months ago by 34k • written 6.0 years ago by ★ 4.4k
98
votes
43
replies
70k
views
27 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 22 months ago by ▴ 90 • written 9.0 years ago by ▴ 280
69
votes
19
replies
69k
views
13 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl identifiers mapping
updated 6 weeks ago by • 0 • written 10.7 years ago by ▴ 180
93,678 results • Page 1 of 1874
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Enhanced Volcano removal of labels
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Answer: What does that dip in the density plot mean from a single cell data analysis?
Comment: What does that dip in the density plot mean from a single cell data analysis?
Answer: What does that dip in the density plot mean from a single cell data analysis?
Answer: Which method is the best for using in "dba.count" in Diffbind R package
Answer: Which method is the best for using in "dba.count" in Diffbind R package
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Recent Replies
Comment: use a list of id to extract sequence from different genomics by LZH289 • 0
thank you!
Comment: What does betaPrior do in DESEQ? by i.sudbery 12k
Those DE genes - is that after a log fold change cut off?
Comment: How to filter VEP results of "missing values" by Yiming • 0
Thank you so much! I found an error with my code. And this works: filter_vep -i VEP_annotated.vcf -o VEP_filtered.vcf --format vcf --fo…
Comment: use a list of id to extract sequence from different genomics by GenoMax 104k
Please use the formatting bar (especially the `code` option) to present your post better. I've done it for you this time. <br /> <img src="…
Comment: gnomaAD exome and genome AF differences by humzakhan340 • 0
The point that genomes are much larger and more computationally intensive to work with is well-taken. However, promoter information is not…
Comment: ERROR [mem_sam_pe] paired reads have different names -- during binning in metaW by swbarnes2 10k
Do you understand what the problem is? Have you figured out which step introduced it?
Comment: gene expression of specifics gene by Bioinformatics1 • 0
Thanks Hyper-Odin
Comment: inquiry related to snpsift by rheab1230 • 0
I have one question related to earlier step where you are formating the .vcf file. You are removing white space and removing format tags ex…
Comment: inquiry related to snpsift by rheab1230 • 0
Hey Kevin, its working now. Earlier I use conda to install the software. But that is not working. So I went to bcftools site and downloaded…
Comment: What does that dip in the density plot mean from a single cell data analysis? by m.sadman.sakib ▴ 100
Thank you very much for the great explanation! Really appreciate it!
Comment: Which method is the best for using in "dba.count" in Diffbind R package by m.sadman.sakib ▴ 100
Thank you very much, Rory!
Comment: How to merge folders that have similar (not the same) names, in a folder keeping by cpad0112 16k
**Before** ``` $ tree . . ├── 123_S1_R1_001 │   └── 123_S1_R1_001.fastq.gz ├── 123_S1_R2_001 │   └── 123_S1_R2_001.fastq.gz ├── 456_S25_R1…
Comment: SNP density plot of aedes genome using bed file by Hamid Ghaedi ★ 1.7k
There is no figure to look at that!
Comment: How to filter VEP results of "missing values" by GenoMax 104k
Looking at the [examples of filters on this page][1] something to try `--filter "LoF_filter not exists"`or `--filter "not LoF_filter`? …
Answer: Measuring pairwise distances between residues/atoms in structural alignment of p by Woa ★ 2.8k
haven't used Pymol for a while but I think you can write a script to automate the analysis rather than doing interactively
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